So.. some of my findings (in offline mode, because reasons)

The game still has a GFWL logic (you can see this when you try to delete saves), that somebody clumsily wrapped with Steam API
It has no clue of wherever the save is. Querying and writing is handled by Steam process
The key file is remotecache.vdf:

if you modify saves with Steam running, when they get passed to the game they'll be "damaged"
if you delete it with Steam running... nothing change (it's probably even stored in memory)
if you delete it (and restart Steam), a new one is created. But the only file mentioned is profile.bin, and game can't see anything else

You can do something by:

making sure there are the specific save#.sgd entries of the save game files you need in the remotecache.vdf (they have to be created manually in-game)
then Steam has to be closed
do what you have to do
Reopen steam (and here I believe here it mercifully updates hashes and all)
profit. Maybe.

Or perhaps you can trick the vdf file. "size" is the size in bytes. "sha" is the SHA-1 hash. "time" and "localtime" look suspiciously similar to unix time

In online mode some additional variables come into play (like -the game that queries- Steam that queries cloud before everything)..
and I guess the trick explained in the article may be the only hope

EDIT: I wonder if this Steam update couldn't have solved something

Topic on Talk:Batman: Arkham Asylum