QB Issue Resolution:

If it is in the make deposit window, you need to deposit it and re-reconcile it to make the beginning balance the correct one.

Resolution for Issue 'Trying to reconcile & Previous Reconc. Discrepancy rpt says I have a deleted deposit. I see it in on cust. ledger, deposit detail report, it applied but Beg bal is off' available: Yes (Solved).
Source: Intuit Community forum.

Trying to reconcile & Previous Reconc. Discrepancy rpt says I have a deleted deposit. I see it in on cust. ledger, deposit detail report, it applied but Beg bal is off: 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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