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Why do deleted or changed transactions still appear on the Reconciliation Discrepancy Report in QuickBooks Online, and how do I clean them up?

Forum|Forum|1 year ago
January 28, 2025
4 replies
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I recently took over management of our QBO account and there were a handful of things from 2024 needing fixing. I believe 11 bank transactions were confirmed instead of matched to the corresponding entry. It looks like maybe this created a fake QB entry to match the bank transaction to, which left the actual QB entry used to print the check in limbo. So I had to unmatch the fake QB entries, then unreconcile them (change R to blank in the Bank Register) so I could find the actual QB entry in the "Find other matches" list. Now these 11 fake entries show up in the Reconciliation Discrepancy Report. I tried to just delete a fake entry and now that one shows up in the Reconciliation Discrepancy Report, getting me nowhere.

There are also instances where I voided checks that were reconciled because they were printed in error and were not deposited.

Then one other instance where the last person voided a reconciled check that did end up getting deposited later on and is matched. For this can I just re-create the entry and swap the match to that one? I have a feeling the initial entry would still show up in the Reconciliation Discrepancy Report.

Thank you.

QuickBooks Online

Best answer by sofiamdc-2341

Deleted or changed transactions still appear on the Reconciliation Discrepancy Report because QuickBooks Online keeps a record of every change made to a cleared transaction, so deleting one doesn't erase it from the report. The good news: this is completely normal and exactly how it's designed to work. The report isn't meant to be empty. What you're really aiming for is a Total Discrepancy Difference of $0.00, and once you hit that, you can reconcile normally even with those historical entries still sitting on the list.

Clearing up the "fake" duplicate entries

To clean up the report, run it, verify each flagged item, and work the list down to a Total Discrepancy Difference of $0.00. Here's how:

Run the report: head to All apps, then Accounting, then Reconcile, and pick your account. If your beginning balance is off, you'll see an alert that says "Your account isn't ready to reconcile yet." Select the "We can help you fix it" link to open the Reconciliation Discrepancy Report.
For each flagged item, double-check that the correct QuickBooks entry is the one matched to the bank transaction, and that the duplicate is gone.
Keep working through the list until the Total Discrepancy Difference shows $0.00. And remember, a deleted transaction can hang out on the list without affecting your reconciliation at all.

Want to dig a little deeper? These articles are great for more details on this topic: Fix issues at the end of a reconciliation in QuickBooks Online and Fix issues with your beginning balance for accounts you've reconciled before.

Voided checks that were never deposited

Mark voided checks that never cleared the bank as reconciled during your next reconciliation. This covers checks that were reconciled and then voided because they were printed by mistake. Checking them off keeps them accounted for, so they won't throw off your balance.

A voided check that was actually deposited later

If a voided check was actually deposited, recreate the correct entry for the deposit that cleared, then swap the match so the bank transaction links to the real entry. So your instinct here is spot on! The originally voided entry might still pop up on the discrepancy report as history. That's perfectly fine, as long as your difference nets out to $0.00.

The adjusting entry that bridged the $1,530 gap

QuickBooks Online creates a reconciliation adjusting entry only when you select the "Add adjusting entry" link after choosing Finish now on an unbalanced reconciliation, and it forces the account to balance. The usual suspects behind a gap like this are: a transaction that was edited, deleted, moved, or unreconciled after it was reconciled, an incorrect or changed opening balance, or a transaction that was manually marked as reconciled. Since $1,530 is a meaningful amount (not just a few cents), it's definitely worth tracking down the source before accepting it. The audit log is the fastest way to find what changed:

Go to Settings (that's the gear icon), then Audit log. (You'll need admin access for this one.)
Select Filter, then set User to All users and set the date range to cover the reconciliation period in question.
Compare the changes against your bank statement to spot what moved the balance. Here are the details: Use the audit log in QuickBooks Online.

To remove the adjustment, undo that reconciliation and redo it once the underlying transaction is corrected. As of 2026, primary admins can undo an entire reconciliation (along with In-house accountants and accountant users): head to Reconcile, select History by account, and choose Undo from the Action column.

Just know this also reverses any later reconciliations and permanently deletes that reconciliation report and its attachments, so download anything you want to keep first. Here's the how-to: Undo an entire reconciliation in QuickBooks Online. Don't have one of those roles?

You can still unreconcile transactions one at a time in the register: Undo or remove transactions from reconciliations in QuickBooks Online. Once that's done, just reconcile the account again. And remember, adjusting entries are mainly for small leftover differences: Enter an adjusting entry for a reconciliation in QuickBooks Online.

Hope this helps clear things up! Once that Total Discrepancy Difference reads $0.00, those lingering entries are just history, and your books are balanced and good to go. If anything else comes up along the way, don't hesitate to reach out.

A

Aldren18

QuickBooks Team

I appreciate the detailed information you've shared, @QuestionForYou. It’s great to see your commitment to maintaining accurate financial records in QuickBooks Online. Let’s collaborate to resolve these discrepancies and achieve precise reconciliation.

Deleting fake entries still appears in the Reconciliation Discrepancy report because QuickBooks retains a record of changes made to cleared transactions.

I recommend reconciling your account once more to resolve these discrepancies. This will enable the system to generate a new Reconciliation Discrepancy report that accurately reflects your current transactions and balances.

If a check has been voided and not deposited, you can mark these voided checks as reconciled during your reconciliation process. If a voided check was later deposited and matched, you can recreate the entry for accurate tracking and replace it with the original match.

To prevent similar issues in the future, ensure that all transactions are accurately recorded and matched during reconciliation. Regular audits of your accounts can also help catch discrepancies early.

Additionally, I would like to share some helpful resources to assist you in handling your transactions in QBO. These articles guide you through resolving any reconciliation issues you may encounter and guide you on maximizing the benefits of your financial reports:

To further enhance your experience with QBO, consider exploring QuickBooks Live Expert Assisted. This innovative service connects you with QuickBooks-certified experts who provide personalized guidance tailored to your needs, particularly in managing transactions.

You can always swing back to this channel if you need help with your QuickBooks entries. Our awesome Community team is here to support you along the way.

Q

QuestionsForYouAuthor

Thank you for your reply, it sounds like I'm on the right track. I realized I could move ahead to reconciling anyway despite the discrepancy, but then I came across another issue.

When looking at the History by account page, I'm seeing that the last reconciliation was performed on 6/6/24 through statement end date of 6/6/24. The time before this was done 4/9/24 through statement end date of 2/1/24. I'm seeing that the ending balance on 2/1/24 is $1,530 higher than the starting balance shown during the 6/6/24 reconciliation, and so an auto adjustment was made to bridge the gap. How does this happen? I did not modify cleared transactions in this date range. Can this be undone?

Thank you.

I

Ivan_G

Moderator

I appreciate you getting back to this thread, QuestionsForYou. I'll discuss the possible causes of the discrepancy that was automatically replenished by QuickBooks Online (QBO).

Here are several factors why there's a discrepancy with your reconciliation:

Modified or deleted transactions after reconciliation
Changes to opening balance value
Journal entries affecting the previous reconciliation date
New transactions entered within the dates before the last reconciliation

To confirm, is there another user in your business who manages your account? If so, they could've been the users who made changes to the reconciled data. We can utilize the Audit log feature in QuickBooks Online (QBO) to confirm this.

Here's how:

Go to the Gear icon, then Audit log.
Modify the User to All Users and set the Date Changed to align with the reconciliation period.
After that, choose All events from the Events field to display all the transactions and potential modifications or removed data from the date range you've set.
Refer to your bank statement for accuracy.

Since the platform automatically made adjustments to resolve the discrepancy, it would be best to leave it as is. However, if you still want to fix the previous reconciliation, you can seek assistance from an accounting professional to guide you appropriately. This way, you can ensure you'll retain precise records in QuickBooks.

For this matter, you and the accountant can utilize this article for the complete procedure for handling this situation: Fix issues for accounts you've reconciled in the past in QuickBooks Online.

I'm also attaching these resources so you can gather more insights about the proper reconciliation process and reconciling data that precede your opening balance:

You can always get back to this thread if you have more questions about handling your reconciliations in QBO. The Community is always here for you.

sofiamdc-2341

Answer

Community Manager

Deleted or changed transactions still appear on the Reconciliation Discrepancy Report because QuickBooks Online keeps a record of every change made to a cleared transaction, so deleting one doesn't erase it from the report. The good news: this is completely normal and exactly how it's designed to work. The report isn't meant to be empty. What you're really aiming for is a Total Discrepancy Difference of $0.00, and once you hit that, you can reconcile normally even with those historical entries still sitting on the list.

Clearing up the "fake" duplicate entries

To clean up the report, run it, verify each flagged item, and work the list down to a Total Discrepancy Difference of $0.00. Here's how:

Run the report: head to All apps, then Accounting, then Reconcile, and pick your account. If your beginning balance is off, you'll see an alert that says "Your account isn't ready to reconcile yet." Select the "We can help you fix it" link to open the Reconciliation Discrepancy Report.
For each flagged item, double-check that the correct QuickBooks entry is the one matched to the bank transaction, and that the duplicate is gone.
Keep working through the list until the Total Discrepancy Difference shows $0.00. And remember, a deleted transaction can hang out on the list without affecting your reconciliation at all.

Want to dig a little deeper? These articles are great for more details on this topic: Fix issues at the end of a reconciliation in QuickBooks Online and Fix issues with your beginning balance for accounts you've reconciled before.

Voided checks that were never deposited

Mark voided checks that never cleared the bank as reconciled during your next reconciliation. This covers checks that were reconciled and then voided because they were printed by mistake. Checking them off keeps them accounted for, so they won't throw off your balance.

A voided check that was actually deposited later

If a voided check was actually deposited, recreate the correct entry for the deposit that cleared, then swap the match so the bank transaction links to the real entry. So your instinct here is spot on! The originally voided entry might still pop up on the discrepancy report as history. That's perfectly fine, as long as your difference nets out to $0.00.

The adjusting entry that bridged the $1,530 gap

QuickBooks Online creates a reconciliation adjusting entry only when you select the "Add adjusting entry" link after choosing Finish now on an unbalanced reconciliation, and it forces the account to balance. The usual suspects behind a gap like this are: a transaction that was edited, deleted, moved, or unreconciled after it was reconciled, an incorrect or changed opening balance, or a transaction that was manually marked as reconciled. Since $1,530 is a meaningful amount (not just a few cents), it's definitely worth tracking down the source before accepting it. The audit log is the fastest way to find what changed:

Go to Settings (that's the gear icon), then Audit log. (You'll need admin access for this one.)
Select Filter, then set User to All users and set the date range to cover the reconciliation period in question.
Compare the changes against your bank statement to spot what moved the balance. Here are the details: Use the audit log in QuickBooks Online.

To remove the adjustment, undo that reconciliation and redo it once the underlying transaction is corrected. As of 2026, primary admins can undo an entire reconciliation (along with In-house accountants and accountant users): head to Reconcile, select History by account, and choose Undo from the Action column.

Just know this also reverses any later reconciliations and permanently deletes that reconciliation report and its attachments, so download anything you want to keep first. Here's the how-to: Undo an entire reconciliation in QuickBooks Online. Don't have one of those roles?

You can still unreconcile transactions one at a time in the register: Undo or remove transactions from reconciliations in QuickBooks Online. Once that's done, just reconcile the account again. And remember, adjusting entries are mainly for small leftover differences: Enter an adjusting entry for a reconciliation in QuickBooks Online.

Hope this helps clear things up! Once that Total Discrepancy Difference reads $0.00, those lingering entries are just history, and your books are balanced and good to go. If anything else comes up along the way, don't hesitate to reach out.

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