Yeah, think the problem is SCOM's big3d is technically older than the 10.2.3 HF1 big3d even though it has a higher code (10.4.xxxx).
I know you will want your SCOM back up soon so the only thing I can recommend is sending a case to support.
TITLE: SCOM's big3d "Version [b}10.4.0.1.0" restarts on 10.2.3 HF1.
Referencing this thread.
They might be able to give you the newer big3d (ex. the big3d my EM 2.3 installed "10.4.0.12.0" and make everyone happy (SCOM won't complain there's an "older" code and will have the most recent big3d code which works with the latest 10.2.3 HF1). Or you might even be able to put a v11 big3d on. However, you would need to get Dev's recommendation on that one.
Like I said, last I heard, they were working aggressively on addressing this versioning issue so we won't have to worry about this anymore.