Spotlight erased external drive?

I have a Western Digital 320 gb Personal Edition external drive connected through USB. Today I started Time Machine for the first time. I noticed as TM was backing up my files from one internal drive to another that Spotlight was indexing my external drive. Didn't think anything of it, indexing is usually a good thing.
Checked the WD drive post TM initiation, and it's empty, by the looks of the gigabytes available, wiped clean.
Questions: How can this happen? Are the files truly gone, or by some trick they'll reappear? I won't restart my computer until I hear a somewhat definitive answer, and potential solution. Thanks!

OK, having not turning off the Western Digital 320 gig drive since beginning this, my Command-I reveals though it is a 320 gig drive and shows there are 0 files, two things to note:
1. It is now formatted as a MS-DOS (FAT 32) drive instead of the original Mac initialized disk.
2. Though the capacity is 320 gb, there is only 120 gb. available, meaning the Mac files/.jpgs/mp3 apparently still exist on the drive, but are now rendered invisible?
Great - invisible files.
SO: Can simply indexing an external drive reformat it to MS-DOS Fat 32?
If so, how do I access the existing files? They do not appear erased.
PROCESS:
1. I plugged in a Mac-formatted external Western Digital drive using USB with 200gb of information on it,
2. started Time Machine to back up to a secondary internal drive,
3. simultaneously and automatically the external drive began to be indexed while starting up Time machine, and
4. now post-indexing it shows 0 files available - how can this happen, how does indexing reformat a Mac-initialized drive into a MS-DOS (FAT-32) drive while still retaining the existing files on the drive?? I am dumbfounded.

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