Kevander.....I would suggest you open up your own thread for this...as this issue has come up before and is solved (to some extent) easily.
You could have many issues here...
But basically, if you copy the old QXP file to your desktop, then update it to 6.x, and save back to server...all will be fine in your world...its the most hassle proof way of updating.
But I would open a thread....as your probably on a windows network as well by the sound of it....and thats a whole other ballgame.
Good luck...stick with it, the benefits outweigh the problems.
BD