This is a problem I raised back in MC21 but I guess was never looked at.
I am wanting to convert my DVD rips to MKV
After conversion I imported and ended up with the following on disk.
\\UNRAID1\Video\Movie\2 Fast 2 Furious\2 Fast 2 Furious.mkv
\\UNRAID1\Video\Movie\2 Fast 2 Furious\VIDEO_TS\
MC has two entries.
If I delete the IFO version in MC it deletes the entire 2 Fast 2 Furious directory even though the mkv file is there.
MC still has an entry for the mkv but it is a dead link now.
Now I can get around this by deleting before I import but I don't think MC should have touched the mkv file.
Thanks