I bet it *should work*, but doesn't for the same reason the quicksaves and autosaves don't work. The Program Files\Steam\userdata\[uid]\22380\remote folder contains the two saves, plus an .ini file. Every time you start the game, steam restores that .ini file--which means your addition of Archive Invalidation's bsa is getting ignored.
edit: I posted a fix here: http://www.gamesas.com/index.php?/topic/1122356-problems-with-save-games/page__st__40#entry16512501
It should work after running that .bat each time you play the game (use it as your shortcut).