I figured out how it patched me up.
I have been playing "offline" for many months, since I don't do multiplayer. I think that on this occasion Ubisoft saw my update level when they updated their Ubisoft launcher. Anyway, it announced an update was available and I said go ahead.
Whether it was a 'new' patch or not was the only 'error' in my post. It was new to me. It would be new to anyone else who, like me, was playing offline all the time.
Fact remains true, the patching will overwrite installed mod files whatever the version level.
I didn't know JGSME had a feature to help so I learned with this experience. I will go back to sleep now, in offline mode.
