Oh, I completely understand how difficult it is to make things backward compatible, especially when dealing with a platform that inherently doesn't support it. I just spent a few years working in a lab where one change to the code could easily keep you from reading any of the old data that had been collected without a considerable amount of double-checks and legacy code.
From a gaming perspective, I also remember getting the bug at the end of QfG4 where you couldn't do the final action that would complete the game. Either I got lucky and the fix incorrectly loaded my old saved game, or some good samaritan wrote a patch that didn't break backward compatibility. To this day I'm still not sure which it was.
From the bugs I've seen posted, and the vast nonlinearity of the game, it's clear that implementing backward-compatibility for saved games simply isn't an option (even if AGS supported it). My concern then is with the individuals who are part-way through the game and then run it from steam one day to find all their progress erased from an auto-update. Is there a way, from the server side, to prevent automatic updates? That way a player could get a notification that an update is available with a disclaimer that it would eliminate their current progress. If the player applies it, then he or she would have been warned, and if instead the player chooses to wait to finish a particular play-through, then no progress would be lost (even if the player would miss out on the bug-fixes and potential new content). One could claim that a user should have auto-updates turned off if he or she is concerned about this, but I haven't yet played a game through steam that lost progress with updates. Granted, my library is quite small. Games outside of steam are a completely different story, but usually those games require manual updates which come with disclaimers.