QB Issue Resolution:

Don’t Delete the deposit. Think of it as an envelope. You can fix the contents.

Yes, Process a Receive Payment for the client as should have been done and make sure it flows to Undeposited Funds.

Then, Open that existing deposit on your screen and use the Payments Icon at the top, to select the Payment. Remove your manual entry on this deposit screen. End with the same Total and it will not Unreconcile.

Resolution for Issue 'How do I replace a deposit transaction that has already been reconciled with a payment from a client ?' available: Yes (Solved).
Source: Intuit Community forum.

How do I replace a deposit transaction that has already been reconciled with a payment from a client ?: 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 already been reconciled
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