Mark,
I'm so confused as to what possibly could be happening. In my understanding, Facebook generally never actually deletes an application. They have ways to block it instead, so deleting it means they've lost some visibility into the app 'as it was', which is just strange.
In any case, there really shouldn't be *any* setting that makes Facebook want to block or delete your app. If there were, there's not really a point in that setting, if you think about it.
Again, I'm sorry to not give a good answer, but I really can't understand what's possibly happening with the information you've provided. If your app wasn't actually being used (or was only used 'lightly' on a website), there's no reason that even if you were doing something 'bad', that Facebook would even notice. The only things Facebook really frowns on are:
* Posting to user's account without their permission
* Tricking users to giving permissions to login
* Stealing user credentials
etc, etc
In general, none of that's allowed by JFBConnect and, more importantly, even if we did, Facebook wouldn't notice that on small sites. They work on algorithms that need a lot of data to understand when things are going bad and a lightly used site doesn't have that kinds of data associated with it.
Again, I hope that explains, but definitely keep us posted.
Thanks,
Alex