Remove TAG (from tag list), remove from other TAG or Remove From This TAG (from brushes tags) have value only to the current working session. When you restart Krita everything is as before the removals. My system is Void Linux self installed with Openbox window manager and spacefm file manager. Krita is the Appimage version.
Hi Avelino, I fixed the issue with system tags not staying deleted recently, it'll be in the next release.