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Do you have images stored next to your media? That may be a way to eliminate unintended replacement of images. You can try locking the media or reducing/eliminating refreshes of metadata as well. I don't have this issue at all, however, most of my metadata comes from outside sources. Once your library is mostly correct, automation of metadata refreshes is almost a moot point -- new media can easily be scanned if you don't already have metadata/images present.

Another thing to try: move the desired metadata provider up the list for fetching images. If you like TVDB better, move it to the top. Fanart? Move it up.