I figured that was one of the changes, as Sins now warns if a saved game is from a prior version.
Good sanity check though as it'll prevent unnecessary crash reports.
Could the file format include any mod info, eg mod name & checksum, so that you don't accidentally load an incompatible game?
Eg: don't attempt to load if
1) saved game used mod but that mod is no longer enabled
2) Sins has a mod enabled but a saved game doesn't use that mod
3) current mod checksum doesn't match checksum from the saved game.
Would be nice if Sins displayed the reason, eg "Requires mod xyz".
Last one may be too strict though, as it might hinder the development of mods.
Eg a modder changes something, checksum is now different and a game that should load may not.