First edit the bank where the duplicate checks exist. On the Interface (second) screen, temporarily turn off the connection to the AP check rec - change the Update AP setting to 'None'. Then go ahead and reverse the necessary checks in BankRec.

Once that is all done, remember to re-enable the AP status updating from the Bank. Also if any entries get generated for GL, those should be removed from the retrieved sub-ledger batch in GL.

FYI - There is a setting in the Bank Rec company profile that will look for duplicate check numbers and prevent posting if desired.