Hi there,

Making sure you're recording your transactions the right way is a good exercise for preventing errors in your books. 

Based on what you've descried, you could go back into your register and record the transactions correctly. If this means deleting the deposit since the invoice was already paid, here's how to delete it: click on Accounting from the left menu > Chart of Accounts > click the account with the deposit > click on the deposit > More > Delete. 

I also recommend contacting an accounting professional to get more info on this. If you're not in contact with one, I encourage you to search for one on our website using this link here. Doing this will help prevent any future discrepancies. Let me know if you have other questions. I'm here to help.