Thanks - I was scared to restart the array. The cache drive filled up when performing a backup of my windows PC, and the mover didn't work. I went ahead and cleared the cache drive and re-attached. I also set all the shares to "No" for cache before.
I needed to totally reinstall the docker, and rebuild the plex server, but everything is back to okay. I've set app data, domains, system back to "Prefer" and ISOs to "Yes", keeping the large storage shares as "No" to prevent this from recurring.