I do not know if my experience will help you, but I went nuts with menus and Activities when I first received my Librem 13v3 with PureOS. The latter would disappear and I could not get any kind of Applications menu.
From my memory–senior moments possible–it turned out if I enabled the “Applications menu” extension, Activities completely disappeared due to an error.
Here is what I finally did:
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Went to Tweaks->Extensions to see if there were any related ‘triangle !’ (sic) error icons. (I could never figure out where those errors were logged.) I disabled those menu-related extensions and rebooted. I wanted “Dash to Panel” but that “Applications menu” extension kept failing with the error icon.
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I eventually found that my system did not have a proper list of the applications in order to construct the menu. This was in /etc/xdg/menus. There was a kde(?) one but no gnome one. Reinstalling gnome-menus finally generated the list that was needed.
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Went back to Tweaks and reenabled any menu-related extensions.
I think things started working immediately, but I may have rebooted.
I hope this might at least give you an idea of where to look.