Looks like there might be a location even tho App numbers dont match. (Steam\userdata\(your number)\205930) In there is two files. It might be these even tho the Number matches Hitman Sniper Challanges number.
[Edited by ServiusTheBear, 11/24/2012 11:51:42 AM]
Found on the steam forums... For steam versions of the game your savedata is located in: X:\Steam\userdata\32769718\205930\remote (numbers might vary)
The filenames are: HM5 (file without extension) savedata.dat
Have just tried backing up and deleting the folder since steam cloud did not upload my previous game and when starting the game today it asked which one to load from, local or cloud.
However, after deleting the folder, steam didn't ask me which file to use (cloud or local) and the levels I had completed before was now locked since steam cloud save was older. Reverting back to my backup of the local files unlocked them and gave back my scores on the levels.