You don't issue a check that will never be cashed; you would enter the Two Things that are offsetting each other. You need to enter the offset = the Reason it won't be cashed.
For example: An Officer needs to be paid and wants to Donate that to the charitable organization whose books you manage. That is an Expense entry and a Donation sales receipt using a Barter Bank and not a real check and not the real checking account. Or, you owe them and they owe you = not a Check Entry at all.