QB Issue Resolution:

Open the deposit and check to make sure it was deposited to the proper bank account.  Also check the date in the Make Deposit window to make sure you used the correct date and not some date later than the end date of your bank statement.

Resolution for Issue 'Invoice paid & deposited but is not showing up on the bank register. Create invoice > Receive payment to the invoice> make deposit. Not showing up on the bank register' available: Yes (Solved).
Source: Intuit Community forum.

Invoice paid & deposited but is not showing up on the bank register. Create invoice > Receive payment to the invoice> make deposit. Not showing up on the bank register: 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 Bank Account
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Error Recovery for Bank Account [Canada]
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