If I'm correct there has been reports of losing saves when updating. The thing is that the staff doesn't seem to know what's causing that or how is it even possible. Only advice I have seen to be given is that everyone should take a copy of his/her save files before updating. The save files can be found if you go to the directory in which you installed the game, choose the "Save" folder and copy every folder that sounds familiar (named after your main character) and you wish to be absolutely sure not to lose.
Infact, it might be useful if you could run the "search" on your hardrives using the name of your old main character and post the results here. It could be that either the old version of the game or the new one is located somewhere it shouldn't be.