Sorry to say but it all sounds quite similar to my symptoms. I didn't get the steering lock warnings but I did get DSC/ABS failure warnings on the I drive screen during the process. Second key made no difference.
The good news (if you can call it that) is that it was a simple <30min £60 job for BMW to recode the part of the ECU to recognise the keys again. The BMW techie I spoke to diagnosed the problem following my description before he'd even used the fault diagnosis stuff, so I guess it's not completely rare if he'd seen it before.
Seems like madness for flattening a battery though.
It's gone - no longer an e90 330i owner