Its perfectly possible that I have been chasing my tail with this. My explanation doesn’t seem to make sense when you take the file permissions into account. Nonetheless crashing out of Darktable while controlling an Eos5D ( mkii and mk iv) has twice made usb cameras inaccessible to gphoto2. I was only able to correct this by recompiling and reinstalling libgphoto2. Maybe the real effect of that was the rewriting of configurations - but surely they should also have been protected by the file permissions.
This loss no longer seems to happen with the 5Dmk iv although tethered shooting via Darktable is very flaky and crashes too easily to be worth bothering with.
I have Darktable running as a child of a (non-root) bash process that opens it in a new dedicated workspace and then waits for it to exit before removing the workspace. I can’t see that as having any effect on the program.