Hah - that's interesting. It's def. reverted to OEM standard UK spec.
I don't think BMW will have programmed it to do as it's not an approved UK modification, so I guess and Indy did it. All other programming should remain locked despite battery removal, but perhaps whatever the Indy did was less stable.
When I fitted my Reinhold it has a habit of locking the door on drive off, did it for a few weeks on an doof an nver since so settled down, but I do think these settings are rather volatile.
If BMW will do it let me know, but expect a £40 bill