AE will round-file your app if they even suspect you have a warrant.
If possible, get AE to defer your application...QUICKLY before they start looking at you. I don't know of any sure way of doing that without raising flags...if you call them and tell them you have an arrest warrant you need to resolve, they will round-file you as soon as they hang up.
The only thing I can think of is to delete your app (if that's even possible) or change your availability date to some point far in the future (like at least a year). After you get this resolved and VERIFY for 100% sure that the warrant is gone, then re-apply.
This is a conservative industry, and AMR is the poster-child for conservative attitudes in aviation.