Good Afternoon Finaco,

Thanks for connecting with the QuickBooks Community! With migrating from Quickbooks Online to Desktop, items may tend to migrate differently and can cause issues. What I recommend is going through and reapplying these deposits to their received payments. Here is how to create a bank deposit:

1. On the Homepage, select Record Deposits / Make Deposits.
2. In the Payments to Deposit window, select the payments you want to combine. Then select OK.
3. In the Make Deposits window, choose the account you want to put the deposit into from the Deposit to dropdown.
4. Check the deposit total. Make sure the account and selected payments match the deposit slip from your bank. Use your deposit slip as a reference.
5. Enter the date you made the deposit at your bank.
6. Add a memo as needed.
7. Hit Save & Close.

From there, you would need to manage the bank deposit, which the article linked goes into further. Another area to look at would be to review prior reconciliation to see what has been affected and re-reconcile the transactions. I encourage you to speak with your accountant as well. 

• Fix issues when you're reconciling in QuickBooks Desktop

Please feel welcome to post a reply here if there are any questions. Talk to you soon!