Prolly a silly question:
Do you backup the .ncf files as well that sits under "\Steam\steamapps" ?
This is seperate to the actual content/data files you are describing.
In the past I've literally just grabbed the folder containing all the game files and backed that up and its been fine. I've never tried with the .ncf files. Probably too late for me now - but I might test it with some small games.
Can you elaborate a bit please, what do you mean by it seperates the content/data files?
I just tested removing and replacing Botanicula and this game skipped the download folder and went straight to common so my old method worked. Perhaps only some games use this new "Downloading" folder.
Double Edit: POW!
Tried to test on another couple of games but they didn't have NCF files so now I'm confuse.