So When I use Fix common Problems I get "Share appdata set to cache-only, but files / folders exist on the array" You should change the share's settings appropriately  or use the dolphin / krusader docker applications to move the offending files accordingly. So what is the appropriate setting for the appdata? Am I missing something else? 

Cache-only or cache-prefer are both good choices. The former will never move files between array and cache. The latter will move files from the array to the cache if there's room for them. I use the latter. If you do the same and run the Mover it should fix your problem, if there's enough room on your cache.