@BrynS 

"Interesting. When you refer to posting the deposit, do you mean the initial correcting journal entry?"

Yes, correct.  BTW, you can create a deposit in QBO instead of a JE.  You may already know this but JEs don't show on many reports.    

"So instead I would credit the clearing account and then cut the new check from the clearing account, not the main bank account?"

No, you still issue the new check from the main bank account because that needs to offset the correcting JE that debited the main bank account.  The correcting JE (deposit) debits the main bank account and credits the Clearing Account.  The new check debits the Clearing Account (now nets to $0) and credits your main bank account.  The next time you reconcile, clear the lost check against the correcting JE and clear the new check when it actually clears.