QB Issue Resolution:

Ideally the Checking account register balance should be the same with your Checking account balance in the Chart of Accounts. If these two are not the same, then, that could be due to a possible data damage. I suggest running the Rebuild Data Utility twice to fix the problem.

Go to File menu> Utilities> Rebuild Data.

Please let me know if this works.

Thank You!

Resolution for Issue 'In the Chart of Accounts, why is my Checking balance different then the actual?' available: Yes (Solved).
Source: Intuit Community forum.

In the Chart of Accounts, why is my Checking balance different then the actual?: 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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