This page should be helpful:
I think I would choose method 3 as described in the page. Rescue the necessary files from your saved folders, and put them into the same location in a new Profile.
A link in the page leads here;
This shows a list of files in the Profiles folder and what they do. You can choose the files you'd like to move from the old Profile (your saved folders) to the new one.
Whenever I reinstall of the OS, I prefer to reinstall extensions and themes rather than transfer them. The only file backed up files used are Bookmarks.html
(in which I have numbers of preferences stored).
' files (Thunderbird address book) are about all that's used from the old Thunderbird Profies folder.
An alternative approach would be to install MozBackup
. This should be able to extract the necessary files from the saved folders (just browse to where the folders are stored) and install them into a new Profile. This takes the work out of things but it might still be necessary to reinstall one or two extensions.