It does go there, and I had no issue with copying it there. A few of possibilities:
Since the file is what the game writes to to track which scenes you've unlocked, try copying it with the game closed.
Make sure you copy and replace the file, rather than having the file copy as "system_data.rvdata2 (2)".
The last thing might be if you put the game in a restricted folder, like C/Program Files. If so, you might not be able to copy and paste the file correctly due to security restrictions in windows. I personally just made a C/blah blah/h games folder to put things in.