This is resolved. I don't know how it happened exactly, but basically when the camera would crash I tried a bunch of things including deleting the config files.
I found a couple of debian packages to roll bakc to for indi-qhy and used those. They didn't work perfectly but they worked well enough for me to achieve what I needed (now the question is, am I missing information in my images? The images I took before all of this were 60mb, now they're 52 ... maybe I'm just overthinking it).
So, for whatever reason those drivers did not auto-detect/write the RGGB filter field into the configuration.
I deleted the configuration, rebuilt it, and now the filter was in there automatically. It should probably be called 'bayer pattern', not 'filter' under the bayer property.

My images can be fixed by running astfits from gnuastro, so I'm very happy about that.

This was a weird misadventure but I learned a lot.
It would really be good to have a repository available that makes things available for rollbacks though.

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