thank you everyone for your comments and suggestions. i did reinstall the sqlite database as per the sticky and that has seemed to do the trick. Oddly though, my previously loaded bookes remained but ive lost the 100 free ones and my SD card no longer seems to work. BUT a small price to pay to have my kobo working again.
I believe you were all were correct - it was probably the two different desktop apps screwing everything up not truely "bricked".
Live and learn i guess!