Me Again with my 2000 lx remote problems

Just an update. My 2000 lx has a manufacturers remote system, however someone added power doors (Codealarm) and therefore it cannot reprogrammed by the conventional method. The remote that I have is fine, locks, unlocks,
but the problem is that when I removed my battery cable the programming in the keys was wiped out and that is why it won't start, I thought it was a remote originally. Is there any way around this problem before I have it towed to a Ford dealership? My main concern is that will I have to have it towed any time I have a battery issue and have the keys reprogrammed? Thanks. Mark.
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