Hi Ralph,
If this is a 'take-on' batch to initially populate BankRec with other checks (ie Payroll), then you're only option is to delete the resulting BankRec GL sub-ledger batch.
For regular processing after take-on, the answer depends on the batch you are importing into BankRec. If the other application (Payroll, etc) is creating a batch with the same GL distributions already posted by that program, then the solution is the same; delete the respective BankRec sub-ledger entries.
On the other hand, if there is more control over how the batch to be imported into BankRec is created, there is an easier way. Use a clearing account (similar to how the Payables interface works) for the other application, rather than posting directly to the bank. This would mean that the imported BankRec batch would only have one detail per check, with the GL account within being the clearing account. Posting this batch 'balances' the clearing account and automatically updates the Bank GL account.
This latter method means you don't have to delete any retrieved GL batches. But again it depends on the other application and how it creates the BankRec batch.