I think that might have been the case? When I checked after updating the game, it showed two copies of one mod (which I could have sworn I only had one of the two turned on, and one was an updated version of the other). Only way to find out would be to try loading the save once again with only the updated copy of the mod.
EDIT: Just attempted to load it with just one copy of the mod, only to have the same error. Looks like Lafiel's explanation is the correct one.