There is an uninstall
option in the Makefile:
uninstall:
-rm -rf $(foreach theme, $(THEMES), $(PREFIX)/share/themes/$(theme))
-rm -f $(foreach file, $(shell find share/ -type f), $(PREFIX)/$(file))
-rm -f $(PREFIX)/share/gnome-shell/theme/$(BASE_THEME)
ifeq ($(IS_UBUNTU), true)
-update-alternatives --remove gdm3-theme.gresource $(PREFIX)/share/themes/$(BASE_THEME)/gnome-shell/gnome-shell-theme.gresource
else
-mv $(PREFIX)/share/gnome-shell/gnome-shell-theme.gresource.old $(PREFIX)/share/gnome-shell/gnome-shell-theme.gresource
endif
I guess the -mv $(PREFIX)/share/gnome-shell/gnome-shell-theme.gresource.old $(PREFIX)/share/gnome-shell/gnome-shell-theme.gresource
could be the relevant part.