"Clearing" a transaction in BankRec generates no GL activity, so I'm not clear how it would mess your numbers.

If you posted a batch in error in BankRec, then enter and post a batch that reverses the transactions that were posted.

Since you exported transactions from Ledger and they are presumably sitting in Excel or a CSV file, a quick way of creating the reversing batch would be to edit that file and flip the sign of all the amounts.