Would there be a way to tell using X tools whether System Settings has two windows?

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xwininfo -root -tree | grep -i systemsettings

This relies on systemsettings/qt putting a usable name on the toolbar (usually does) - since it's a toplevel window, there's no mandatory parent/child relation on the X11 layer.

If above doesn't work, i could only think of a diff between

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xwininfo -root -tree

before and after closing systemsettings

I can confirm that on my system at least, "xwininfo -root -tree | grep -i systemsettings" works fine. Could someone affected by the issue please try running it and posting the output they got?