Done both of those, the problem eventually comes back.
For example, Affinity Photo, installed in /Applications is already running. I right click a .png file, choose Open With, choose Affinity Photo from the list - and instead of opening it in the version already running, it tries to open the copy from the bootable mirror backup (Chronosync).
Drives that you can't search on in Finder, because they're in spotlight privacy, have apps stored on them populate the Open With contextual menu, but the system is refusing to direct Open With to anything in /Applications on the boot drive.