You have an option to print your reconciliation.
Backup your AP data.
Print with your reconciliation by setting all record types clicked on (O/S, Void, etc), with a valid cutoff date, to when you want to purge the data.
Suggest that you print to a PDF record, say using CutePDF, or to a file. (Save a tree).
If all record types have been enabled, at the end of printing you will be prompted to answer yes or no to purging all completed data, so all outstanding cheques will remain.
Best,
Brian