To answer the question. No problem. The file system for data does not matter. Some windows files can't be read by Linux programs because the program the runs them exists only for Windows. Even most of those can be worked around. Wine, export into Linux acceptable format etc.
What most of the rest are saying is that it is hard to wipe a system and not loose some data. That email from now dead Grandma with the photo of you as a 3 yo no one else had, your Bookmarks folder, email address list, etc. Oh, the pain!
My tactic has become:
1. Ghost my old system to an external USB hard drive using the Ghost program on Hiren's.
2. Back up the entire user's folder in docuemts and settings to whatever size medium is required, DVD, CD, External drive.
3. Back up the Favorites or Bookmarks and the addressbook as html or csv file.
4. If they have a specific directory for Music, images, etc, back that up.
Ths way you have redundant backups of the most importetn nonrerecoverablefiles and can recover the entire systmem if needed.