I thought I'd just share my experience with you all. [This is using the io method suggested in the unpacker's readme]
After I changed the ReligionStarter trait to apply to characters family instead of characters general, all generals in my savegame had the trait working just fine.
Therefore, any changes to the character traits file will have a retroactive effect on any savegames.
However, I am not sure if the same applies for other files, but it could well be!
