Dealing with Cash-In-Transit when upgrading from 11i to v12

We are upgrading from Oracle 11i to v12 but are not converting cash-in-transit items (i.e. outstanding checks) from Payables.  I am hoping that someone can offer guidance on an efficient way to account for these checks as they are cleared at the bank and come through the MT940 file.  Since the payments will no longer be the in the AP system, there is nothing to reconcile to, so we will have to track the checks in a spreadsheet and then manually book a journal entry to clear the checks as they come through. 
Is there a possibility in CE to create these outstanding checks (without going through AP, since we have already cut the checks) just so that there is something to reconcile with?