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hey, not an expert here but it sounds like there's no issue with the HW if the livecd & fresh install works well.

During initial install some config files are populated based on what you do during the livecd installation (this is normal) so during an update some package may have replaced those config files with a "fresh" one. Your livecd probably populated it with the 3rd monitor detected but a fresh config file most probably doesn't have that written down by default.

Anyway, all that just to say that you might want to find the file where the 3 monitors are configured on a fresh install and save it. After an update put the file back (and notice if it changed). Which and where that file is-at idk. I think it's different for wayland vs Xorg.

Some breacrumbs: use xrandr to get some info. I would assume some gsettings could also shed some light.

Hope this helps!