Yes...and No... Some folks have reported being able to recover their saved career data, and reinsert it after installing SH3 with GWX 2.0...I'll quote from another forum I frequent..
managed to get my old career to work by saving my "Captains Name" career folder out of the My Documents/SH3/data/cfg/Careers folder. I then did the uninstall/reinstall/patch/install GWX 2.0 routine. I then started a new career and a patrol and then saved/exit it right away. This sets up the SH3 folder in My Documents with all the needed settings. I then took the saved "Captains Name" folder and replaced the new one created in My Documents/SH3/data/cfg/Careers with it, and it worked.
another quote...
.....I think it all depends on the Data which is in your "saved career". If there is a reference to some sunken ship etc. that is listed differently in GWX 2.0, then it will not be recognised and will cause a crash.
That is probably why it appears to be a little random as to who is seeing some success with recovering save files in GWX2.0 or not!
and one more..
..I believe the GWX team said your old career might work in 2.0 but, there was no guaranty that it would.
and...some have said it don't work...so there ya have it.
If I were you, I would do a duel install of SH3...just for GWX 2.0...and leave your other one alone