I thought I deleted a bank deposit from the bank register but now it will not let me delete received payments on that invoice. How do i fix this?

I'll share some clarity on how to manage your received payments linked to an invoice, EE.

Before we proceed, could you please provide more details about when you attempted to delete the transaction? Have you encountered any error messages? Any additional hints would be appreciated. 

If you've received the following prompt below: 

Please note that you can still proceed to delete the payment. The notification only serves as a reminder that the transaction you're about to delete is linked to an invoice in QBO. By deleting the payment, the invoice will no longer be marked as paid, and it will revert to an unpaid, reopening in your records.

If you mean anything else, feel free to reply to this post.