I think this doesn't affect me because I never updated past 1.0.0, and consequently never had the extra banks. Moreover, the SoundTower editor was too buggy for me to keep using for gig prep, so I never tried overwriting the factory banks.
As as result, as far as I know, there was also no need for me to worry about reinstalling factory banks 1-8. Laziness worked in my favor!
On the other hand, I'm now playing around with 2.0 and have loaded the alt tunings update + factory & user banks 9-G (I'm mildly surprised it wasn't configured to hexadecimal enumeration, i.e. 10=0, 11=A, 12=B, etc). The new sounds are pretty sick! Haven't had time to jump into the new features, but will this weekend for sure.