I had to do a full reinstall on a Windows PC yesterday every document and Thunderbird email had been backed up dailly to CDRW and and twice weekly to a FTP server using Cobian Backup --- it all restored without a single missing email or document :-)
The Emails and Thunderbird settings had been saved maunually with MozBackup

Both programs are free and higly recommended.

http://www.educ.umu.se/~cobian/cbu6.htm
http://mozbackup.jasnapaka.com/