QB Issue Resolution:

Regarding with the concern that you have, you can use the resolve difference to record the erroneous deposit then record  transfer to reflect in your QuickBoooks.

 

Here’s how to do it:

  1. On the left navigation pane, select Banking.
  2. On the Bank and Credit Cards page, make sure to select the Bank Account  with the transaction.
  3. Find and select the relevant Transaction on the For Review tab.
  4. Click on Find Match radio button.
  5. On the Match transactions window, select the checkbox of the appropriate Invoice.
  6. Click on Resolve Difference to open the Add resolving transactions fields.
  7. Select Add new transaction.
  8. From the drop-down list in the Category field, select the Bank Fees expense account you created.
  9. Enter the Amount of the bank fee.
  10. Once done, select Save and close.

You can also assign, categorize, edit, and add your downloaded banking transactions, this article can guide you: Assign, categorize, edit, and add your downloaded banking transactions.

Resolution for Issue 'I recently deposited two checks to my bank account and it pulled in to the online bank feed as one single deposit ($200 +$100 = $300). The problem is one of those checks was deposited in error, while the other does match an open customer invoice. When I go to “match”, it won’t let me match $200 to the open customer invoice because the $300 deposit amount is $100 more than what the invoice states. How do I “clear” that $100 deposit? Through my bank I set up an ACH payment to have the $100 withdrawn from the account and transferred to the correct one.' available: Yes (Solved).
Source: Intuit Community forum.

I recently deposited two checks to my bank account and it pulled in to the online bank feed as one single deposit ($200 +$100 = $300). The problem is one of those checks was deposited in error, while the other does match an open customer invoice. When I go to “match”, it won’t let me match $200 to the open customer invoice because the $300 deposit amount is $100 more than what the invoice states. How do I “clear” that $100 deposit? Through my bank I set up an ACH payment to have the $100 withdrawn from the account and transferred to the correct one.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Banking
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