Didn't see this any sooner, sorry. I don't look in the HDR/MDR section much, since I rarely use mine.
If the battery went out, or the BIOS settings somehow got changed, that could cause all kinds of problems including what you're describing.
Did you check that your BIOS settings match what's described, here?
https://www.sonido-7.com/d8b/files/hdr_and_d8B_new_mb_bios.pdfIf that doesn't fix it, you might have to reinstall the OS. (I'd try pulling out all the I/O cards and starting without them for a test before that... just in case one of those cards has an issue. Also, make sure the firmware chip on any DIO8 cards you may be using matches - ideally v2.1. Otherwise you might get bit-depth issues (16-bit only) or other odd misbehavior).
As for your other question... I'm not aware that the HDR would allow you to route it's tracks to different outputs. AFAIK, it's a 1:1 mapping for all the channels from 1-24. I think the idea was that an HDR would be used with something like a Mackie D8B and you'd be re-routing the signal on the D8B side.
...but quite honestly, I'm not sure if there's another way to re-route within the HDR. Never noticed that, but I never needed it, so I wasn't looking (and am not where my HDR is right now).
Best of luck!