Admin Res Judicata -- well, not - but an interesting issue
Unfortunately, the court gives no details, but it appears that one special exception was granted, appealed, and then expired during the pendency of the appeal. Another was applied for and denied, though we don't know if this occured while the cert petition was pending or while the applicant/church was trying to appeal the legal decision in the first case.
Interesting - the first cert (obviously 3d party) was claiming admin res judicata against the granting; the circuit judge denied as moot (because of the expiration) and also made a comment that the Board had erred in granting the exception because of the admin res judicata issue. The church took the issue to the Fourth on that issue. The Fourth declined on the basis that of mootness but also because the Board had denied the later application. It therefore declined to rule on the res judicata issue. What we don't know is whether the later denial is up on appeal in the circuit court. If it is, the res judicata issue may be coming back.
See the problem? If the first special exception expired only because the church didn't want to go forward while a cert petition was pending (remember Shidell, you don't want the approval to expire just because of the petition. That creates a situation where attacks on an approval can succeed simply by drawing out the proceeding until the approval expires.
And if it does expire, you re-apply, and then get denied (maybe by a new board, maybe by more developed politics and maybe because the application really didn't meet the standards), you'd want to argue in a cert proceeding against the denial that res judicata applied to the grant, and that the "reapplication" should have been granted absent changed circumstances or standards. This is untried grounds, really - the cases are somewhat all over the place and most of the ones I recall involve attacks rather than defensive use of res judicata (neighbors complaining that a second application shouldn't be approved rather than applicants claiming they should be).
Practice point and future litigation issue: if you're representing an applicant for a special exception (or variance or conditional use permit), get it, and the decision is challenged in cert by a 3d party, you probably want to ask the local government for a stay pending the appeal - yes, as the applicant - so that your time doesn't run out (if you're in a jurisdiction with a short fuse on SEs). [Of course you could take your chances and proceed on the approval, but if it involves construction activity and investment rather than mere use, I wouldn't recommend it to a client).
I'm guessing that many jurisdicitions wouldn't know how to handle this today, and would say they aren't authorized to grant a stay. But look at Fl. R. App. P. 9.190 - the provision for stays of decisions NOT taken under the APA provides that tribunals have the authority to grant them under appropriate terms. But you might end up having to ask the court to use its plenary powers to stay the decision if the local government won't.