Eos 3.2.8, merging in resources and media, where some of the assets already exist in the current file, results in those duplicate assets being moved to the root directory and prevents them from being organized (drag and drop into a folder has no effect, but can move other, freshly merged assets just fine). Eos must be closed and reopened, where they will show up back in their previous organizational hierarchy. Possibly only occurs when merging in show files from before the media organizer existed.