I tried fsck.vfat and got many instances of the following:
[filename]
  File size is [large number] bytes, cluster chain length is 0 bytes.
  Truncating file to 0 bytes.

And:
[filename]
  Contains a free cluster ([large number]). Assuming EOF.

I said no when it asked if I wanted to correct, I said no since now I'm
worried that letting fsck do it's thing would really ruin the disk.
I'll try that before I reformat, but I'm still holding out hope that
someone will help me figure out what the heck is going on.

-- 
vfat external hard drive goes read-only during rsync
https://bugs.launchpad.net/bugs/477773
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