All progress lost in arc, and well anything.
win7 64bit, updated from (first version at release) to 2.08 - not steam version.
Files in ..{user}\my documents\creeperworld3\data\ are there with dates from January 2014 (but strangely none from today)
..{user}\appdata\roaming\creeperworld3\log.txt attached...
There's nothing odd in the log that I see. The update also doesn't touch anything with game progress files, etc. (it just overwrites the exe and related files in the installation folder). So I'm at a loss to explain how the progress would have been reset...