Also have the Pluggable tb3 dock and use 2 external monitors via it (+ another separate monitor).
What you described sometimes happens to me too, but definitely not multiple times a day.
If you don’t have it yet, I recommend purchasing SwitchResX software, as Apple’s own display management tool is garbage. What you can do is create custom “Display Sets” which are arrangements of monitors and custom settings/resolutions which you can then turn on/off. Ocassionaly a monitor will disappear, but then doing a “Detect Displays” in SwitchResX usually fixes it for me.
That software has largely made a lot of my monitor issues like saving layouts go away.