In my payments to deposit account there are 3 years of past transactions that were migrated from old software that need to be cleared. How do I clear them?

Thanks for reaching out, @info-portcityele.

How are you today? I hope all is well. 

In QuickBooks Online you can clear the deposits right from the account register. I'm including some steps below to walk you through the process.

1. Go to the Chart of Accounts and locate the deposits. 
2. Under the check mark column, click on the space repeatedly until you see the letter C.  
3. Tap on Save. 
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Please know this will not affect your previous reconciliations. 

Here are a couple of articles for your reference about reconciliations: 

• Learn the reconcile workflow in QuickBooks
• Reconcile an account in QuickBooks Online 

Let me know if there is anything else I can assist you with. Take care and have a wonderful day ahead!