QB Issue Resolution:

Go to plus sign>bank deposit. You have a customer payment entered to that acct. but not deposited.  You need to find the deposit (it is in there already somehow because you reconciled already) and update the deposit with the customer payment and remove the line item that is in there and was reconciled.

Resolution for Issue 'How to correct undeposited funds? I have reconciled my bank account through December 2016. I show a balance in undeposited funds amount for September – December. How do I fix this since I have reconciled?' available: Yes (Solved).
Source: Intuit Community forum.

How to correct undeposited funds? I have reconciled my bank account through December 2016. I show a balance in undeposited funds amount for September – December. How do I fix this since I have reconciled?: 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.

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