I was under the impression a C&R only stays a C&R if it is in factory configuration. If a rifle is damaged, broken, had parts removed, etc and is 'rearsenaled' into factory configuration, then it is back to C&R status. I'm not sure if that only applies to C&Rs that are not C&Rs by age, because it would see that even if you modified a rifle, then the new configuration would still be on a receiver that is 50 years old and would still be a C&R.
As for the California mod, I believe that falls into adding to the configuration, like putting a scope on it. If the rifle was modified in any way, which since it was bubbaized I am assuming it is, it's kind of hard to take off the added feature, especially if that added feature is a shortened barrel, removal of wood, etc.
Of course I don't know the laws very well either, so I could be wrong.