That seems very odd. Doesn't any external HD connected to an Airport Extreme (or Time Capsule) need to be formatted as JHFS+ (i.e., OS X extended, Journaled) ? If that is true, it seems unlikely that a PC would be able to "see" the files on it (unless you had some extra software to read HFS+ filesystems on the PC)...
So I'm wondering what filesystem the disk is formatted in (perhaps I'm wrong about the HFS+ requirement)?
Oh, wait, maybe you mean "The files are still there as I connected the HD directly to my" Mac? (Sorry, I always interpret PC to mean a Windows machine.)
Either way, I don't know what's happened, unfortunately -- I've never had that happen. Maybe silly question, but have you tried restarting (or power off/on) the Airport Extreme? Weird.