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Nevermind. I just uninstalled it and reinstalled it. I lost all the media files in my upload dir, but luckily I have backups made everyday so I just have to download the files for that dir and upload them again. I still have no idea why the upgrade would wipe out the player code, and even when I put in the correct code for the players it still wouldn't work.
Anyway, I'll just upload and catagorize them again. Nothing much else to do.
If anyone knows how to prevent this from happening again or maybe a more "safe" way to update the module for the next (if there is one) release I would appreciate the feedback.