Yeah you can set PLEX or MediaBrowser to also store stuff outside the movie folder or on another drive (like SSD)
But honestly I would not worry about it. I chased those problems before and as long as the server is idle next time (like middle of the night) it will complete successfully. The error doesn't mean your entire flexraid array is bad either- it just means that one file. If you restored you'd be ok anyways. This is just the problem with snapshot raid, it's a snapshot. Anything that adds or deletes won't mess anything up, but files that change and still exist will throw an error. Only way around it is to not use the server during the process (or run the process again when you are done using it) or convert to a real time raid solution.