I haven't see any Windows Update reset audio sample rates. If you've run into this, please LMK what update # did it so I can check into it.
I run my 2408mk3 and 2x 24 i/o at 96khz and use for both DAW use and Windows audio. To do this, I made sure that *every* port, in and out, was set to 96. As I recall, it took a reboot for the MOTU to properly sync this, but it has worked well ever since.
It took a bit to make sure I had the same on all, though. Then, I set all my DAWs (I use/test a bunch) to use that same sample rate with ASIO or WASAPI. Same sample rate in every app and OS works best.
44.1/48: I've found in the past that my MOTU did not treat those the same. They worked, but played slower when you had them mismatched. The MOTU device would show a different sample rate vs Windows and would get a bit confused.
Pete