This one time I'd disconnected the battery to reset the computer in my old E39 and by mistake the trunk closed. I was stuck and couldn't do anything about it.

I had two keys the spare key and the master key of course. The spare key didn't work when trying to unlock and lock. The master key worked like a charm even with the battery disconnected. Locked and unlocked normally from the trunk and drivers door

I know this isn't the same case but worth trying if you aren't already using the original key. Also why not try and reprogram the remote key? You never know might get lucky!

Sorry for not being able to help much