Strange.
I had mine in for the battery monitoring update some weeks ago (yes, I have been naughty and skipped that for over 1,5 years of nagging by BMW/Mini in the car screen, in my Mini app, by mail, and even by postal letters - all except personal phone calls), but all my bimmer code settings remained 100% as before the software update (like my auto-fold of mirror, remembering drive mode, and seat heat temp mods, etc).
I even left my OBDLink CX in the OBD-port (they did not complain about it, or my mods).
What I did get wiped was the personal settings for the short cut buttons, etc. Had to redo all my short cuts.