“I believe we are double counting Square deposits and that has been an issue before”

Let’s review one example:

You sell by Square, and that is your Settlement agent.

So, in QB, you either use Sales receipts, or let the banking reflect it is income. Not Both.

Sales Receipt that generated income, with Square […]

Resolution for 'banking reflect issue: 'Why do my books never balance?' available: Yes.

The banking reflect 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 banking reflect issue yourself by looking for a resolution described in the article. If it is a complex banking reflect issue or you are unable to solve the issue, you may contact us by clicking here or by using other banking reflect support options.

For more information about resolving issues related to banking reflect in Quickbooks/QBO or to get support for the issue 'Why do my books never balance?', click the link below: