Hello and thanks advance for any support; it's a bit of a read, but I'm hopeful a simple fix exists...
A few weeks ago, I decided to batch process hundreds of VOB files into MKV equivalents using MakeMKV and an applet program called MKV Batch Converter. The process renamed each VOB file (e.g., "25th Hour (2002)\VIDEO_TS) into an MKV file within the same parent folder (e.g., "25th Hour (2002)\25th Hour.mkv") and I manually deleted the original "VIDEO_TS" and "AUDIO_TS" files. None of the other metadata/artwork appeared to be modified during these conversions, however I recently discovered that Emby Server generated a second NFO file for many (but not all) of those batch processed movies. The duplication involves one NFO title which matches the MKV file name (e.g., "25th Hour (2002)\25th Hour (2002).nfo) and another which seems to resurrect the ghost of the previously deleted VIDEO_TS file (e.g., "25th Hour (2002)\VIDEO_TS\VIDEO_TS.nfo). This dynamic has now made the MKV movie files unplayable on the server ("Video Error - There was an error playing the video"). Interestingly, the trailer files all seem to play fine on Emby Server, regardless of folder structure (some in the their own "Trailer" folders, e.g., "25th Hour (2002)\Trailers\trailer.flv" and some within the parent folder itself, e.g., "21 Jump Street (2012)\21 Jump Street (2012)-trailer.mp4").
I originally discovered this issue in Emby for WMC when many of my local trailer icons disappeared and hitting "play movie" would instead play the trailer. I became curious whether a trailer had to actually be within a "Trailers" subfolder for EMC to recognize both file types. I tried to triage the issue for hours until I realized that the common denominator was not the form of the trailers folder structure, but instead that those media folders with two NFO files were causing different playback issues on both the server and client side.
Notably, more recent library additions I have made--not conversions from VOBs, but straight rips to MKV--only have one NFO file within the parent folder and play/display perfectly fine in both Emby Server and Emby for WMC. For the problem movies, however, even when I try to manually delete the duplicate VIDEO_TS.nfo file, Emby Server immediately regenerates it.
I could really use some advice on how to permanently remove these duplicate NFO files (and prevent regeneration) so that I can (1) watch trailers AND movies in Emby Server and (2) don't have to relocate every trailers file into its own "Trailers" subfolder for EMC playback. Screenshots of folder structures and Emby Server metadata settings attached.