Dynamics GP 2013 SP2 introduced the ability to reconcile checkbooks, even when there is no activity in the checkbook. The nice thing is that you don’t have to configure anything special. Simply reconcile the checkbook as you normally would. When you hit the reconcile button it updates the last reconciled date and prints the reports.
Weekly Dynamic:Reconcile Checkbooks with No Activity
Tips & Hidden FeaturesGeneral Ledger & FinancialsPayables & ReceivablesGP 2013
Archived post from 2013. Dynamics GP and the links it points to have changed since; check current documentation before relying on version-specific steps.