You can try entering a General Journal Entry adjustment. On the GJ Entry debit and credit the same cash account used on the bounced check. This basically will show the check amount being redeposited and taken out again. This will be treated like a wash.  Which is just to show the money going back in and out again. So, the balance will still be the same. Do nothing to the original check. Since it actually ended up going thru.

On the General Journal Entry adjustment you can enter a description. Just so that you'll have a reference as to why this adjustment was done.

When you reconcile this cash account should see 3 entries listed.  The GJ Entry adjustment under both deposits and  checks. These 2 would be checked off to create the wash and not affect the bottom line balance. Then you'll see the original payment under checks. When this one is cleared it should reduce the balance as normal.