Used my windows for the first time since getting the car back this morning and the one touch seems to have dissapeared.

The battery has been disconected while the car has been repaired as the clock and mulitfunction thing have all been showing wrong info so could this have caused the loss of the one touch windows?

Can this be sorted with vagcom?

On disconnecting the battery some functions are deactivated. ( p185 manual ) This includes the windows. ( p48). If you do not have the manual I could post the details

If you bring the windows all the way up and then pull the toggle switch back up again, the send the windows down and push the toggle down again once it is all the way should solve it. If it does not work then fiddling about with the window switches normally does it.