How do define a cancelled cheque run? Are you using the Print Post Checks and Advices to print checks or a Manual Check batch to process cheques?

Adagio Payables does not write unapplied cheques to vendor records if you choose to cancel posting. So if you could desribe in some more detail the steps you followed in cancelling the cheque run, perhaps that could shed a little more light on things.

What version of Adagio Payables are you using (look at the Help menu and choose About)?