Missing data

I had to use mybook live to restore a hard drive. I did not know the programs weren’t backed up, but what happens to the data from the non-backed up programs. For example, if you have data in C;\program files\program\user data, where does the user data go when the program doesn’t exist? Does it remain on the back-up device until another restore, or was data from those programs (not in my documents) never originally backed up?