No, they were there. The files are there. They played fine in both MC and in other players. I can manually copy them over to the proper directory, and I can create, edit, and save text documents in the proper directory. I was exhausted so I didn't fully report the steps I had taken.
I fixed it though... There was something else that had happened that I hadn't explained which turned out to be related.
Before I was able to try to sync to my generic handheld last night, MC crashed on me when analyzing some files (building thumbs I think). The JRWorker process got stuck and pegged a core of the CPU. This has happened before with this machine when it encounters corrupt MOV files. I think it is actually a bug in Quicktime, but it only ever manifests itself through MC. Either way, the process got stuck and (as usually happens when this occurs) I wasn't able to manually kill it using Process Explorer. I had to forcibly shut the machine off. Now, at the time when it got stuck, it was analyzing the generic handheld's folder full of files.
Turns out, the drive got "dirty" and some bizarre error was apparently causing this (but like I said, sporadically). Doing a repair on the disk (fsck -fy in this case, since it is a HFS+ formatted partition mounted via MacDisk) fixed it. So, if you get similar errors, try checking your hard drive for errors.
This too might be a good one for the Weird and Wonderful thread...