QB Issue Resolution:

Banking->Deposits. Hit previous until you see the deposit you want to delete. Choose Edit->Delete to delete it.

Probably a good idea to choose File->Backup first, just so you have a known safe point.

Resolution for Issue 'Deleting check register entry' available: Yes (Solved).
Source: Intuit Community forum.

Deleting check register entry: 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 Deposit
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Error Recovery for Deposit [Canada]
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