@BrynS 

Forgot to mention that your deposit that credits A/P should show up as a bill when you go to Pay Bills.  Also, the re-issued check that was assigned A/P should show up as a vendor credit.  As long as the re-issued check is dated the same as the deposit, and you apply the A/P credit created by the deposit to the A/P debit created by the re-issued check, you shouldn't see an Unapplied Cash Payment Expense in your P&L.