Macbook was fixed, paid for backup, files missing

On friday my computer shut off without warning while i was on the internet. I took it into the apple store and the genius guy thought that it might be the magsafe. So I had the magsafe checked out because no matter what was reset the computer would not start. The magsafe wasnt the problem, they thought it was the logic board. So I brought in my western digital external drive and paid apple to back my computer up before they sent it away to be tested.

on wednesday i was called and told my computer is ready. So I rushed to the store and grabbed my compter and the external and rushed them home before I had to be to work.

that night i went to look for a file on my computer and it was gone. in fact a large portion of my files were gone. so i went to the external and did a retrieval. it loaded the folders but not the files.

to get to the files i have to go through finder, and follow that chain until i can get to my files. My problem is that I still have files missing. It doesn't look like they backed it up since my last backup....what can i do, i'm missing some important artwork that i did for clients and contests. My father and I feel like if i paid for the service than why wasn't it done properly.

any suggestions because the phone line is no help. should i take it back to the store?