I doubt they will review your application without the fee - I would assume that the status of your applications would change to 'incomplete', unless of course, they're slow to realize that your cheque has bounced.
You need to mail out those cheques as soon as possible. If you wait for them to contact you about it, it could take a very long time. You might also want to attach a note to the new cheques, in case whomever is processing the incoming mail gets confused as to why you've mailed two application fees.