QB Issue Resolution:

JE means you are making More entries. To Delete entries, you just delete them. You also can Undo  the last reconciliation.

Resolution for Issue 'We accidentally reconciled a sub credit card account that is actually duplicate transactions. I identified them but how do I delete the duplicate charges?' available: Yes (Solved).
Source: Intuit Community forum.

We accidentally reconciled a sub credit card account that is actually duplicate transactions. I identified them but how do I delete the duplicate charges?: 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 actually duplicate transactions
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Error Recovery for actually duplicate transactions [Canada]
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