Question on Time Machine, reformatting my external

I currently have a external hard-drive that is unusable for Time Machine because it's not formatted correctly.

Normally, no big deal, I would just move all the stuff on the external to my mac, format the drive, and move everything back.

Here's the problem - my entire itunes library is mapped back to the external drive in several folders.

If I reformat, and move the folders back unchanged, will itunes "remember" the mapping? I'm worried about a library full of exclamation points.

Thanks for any help!