Hi!
You are taking a risk not removing SHIII, but you can still make a try.
Begin with totally removing all saves under "my Documents/SHIII/...etc etc.
Remove the whole SHIII-folder and throw it into the bin. => All old careers wiped out

.
Then install GWX2 and start a new career => New folder is created.
Q: Do you use SHIII Commander? If not, you really should!
Good luck
/OB
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SHIV:TMo 2.5, RSRD, SCAF OLC, Ralle's modpack
SHIV: WDAD, Med Campaign
SHIII: GWX3 GOLD, OLCII Gold, ACM-reloaded interface mod, SHIIIcmndr 3.2, Full Realism/DiD
SHIII: LSH3 2015
Cold Waters with all bells and whistles
Finally SHV but still unmodded and still a noob....