Usually when you lose several systems in a bmw from messing with the battery its because the explosive bolt/positive battery cable gadget was damaged.

Try turning on something that isn't working and wiggling the positive cable at the battery clamp while the cars running. See if that makes whatever isn't working go back to working and look for sparks at the connector.

The thing is designed so that in the event of a wreck it shoots the main cable out killing the fuel pump, starter, etc but keeping power to the windows, hazard lights etc.

Yours seems to be backwards but the split seems to be along those lines is why I think the problem might be there.

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