If you're really worried, copy the SH3 file under 'My Documents' elsewhere before you install the mod. All your career info should be in this folder (SH3 defaults here unless you've modded to move it).
If anything does wrong, paste the saved file back into 'My Documents'.
I added SH3 Cmdr after GWX 2.0 and had no problems, but better safe than sorry...
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