I once had something similar happen where content suddenly disappeared from my Included Runtime. It turned out that somehow an older version of that Runtime had ended up replacing it. I honestly have no idea how it happened, and I never found the actual cause. In the end I simply restored it from the backup on my second PC.

Unfortunately, I'm out of ideas at this point. I really do understand your frustration, but I'm afraid I can't offer any more useful suggestions. I hope support or Ken can help you get everything working again.

One small thing though: for some reason, most of my scripts never show up in the Script menu on my system (Ken's are actually the exception). I always run them from the Python palette instead. I don't know if that's any help, but I thought I'd mention it just in case.