You are right to Avoid JE for most everything in QB.
This isn't really a big issue at all: "If I delete the transaction, it will affect my reconciled month."
Here is how you manage this bit of Housekeeping:
Make the replacement entry, so you confirm it looks right. Then, Delete the JE. Now you use the same ending balance from the most recent statement you used to reconcile, or wait until your Next Reconciliation. Either method is fine. In either situation, you will ignore the beginning balance because that is the Net of all previously Cleared transactions. You know you affected this status.
If you use the most recent reconciliation ending balance, set the date to one date later than you already used for that statement. That way, this is its own Mini-Reconciliation or Interim Rec. Now checkmark the recreated transaction which you know previously had the status of cleared. If that is the only thing you needed to do, the difference is now 0. Done.
If you want to wait until your next regular reconciliation, you still ignore the Beginning balance. You still reconcile as usual, but you have the recreated transaction to also Clear. You should be at a difference of 0, as usual. If you are not, the Recreated transaction would not be the suspicious entry, since you already confirmed your entry was properly replacing the wrong one. So, go ahead and do only that interim rec, after all, and then you get on with figuring out this Regular cycle's details.
