Hello ANV,
If the cheque has not "left the building", then destroy it and delete the error batch.
If you have sent the cheque to your vendor and they have cashed it (meaning that you paid the same invoice twice) then edit the batch and turn the cheque type into a pre-pay so that you have a credit balance on the vendor's account.
Otherwise, create an adjustment batch to adjust the vendor's account to reflect its current status and post the adjustment batch, giving the doubly paid invoice a current amount.
Then re-post the cheque batch.
The fundamental question is whether you have actually paid the same invoice twice.
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Andrew Bates