why does it have to be this difficult?
remind me why you need to access this in your pc, and why you require root in first place.
I haven't used my N9 for a while but if i am not wrong, isn't everything, the config files and database stored in the home (/home/user) somewhere? (better ask Cepi for the exact location)
you could easily use a file manager (like filecase) to access these files. and even if it is not in home, you can browse the root directory too from filecase itself.
btw, i had an old copy of /home/user/MyDocs/Whastup/.backup. I couldn't find the database there.

Or is it that you have already checked this and not found anything and want to attempt file recovery, which i think might not work as you have been using the phone for 3 months, you say. The database probably has been overwritten during this time.