but the same file is available in the terminal:
ls -l /volume1/DiskStationMedia/VideoStation/serie/Fortitude/S02/Fortitude.S02E10.German.DL.DUBBED.720p.BluRay.x264-AIDA.mkv
On which version of DSM are you experiencing this (DSM 5/6 or DSM 7)?
Does the system user running the PMS (usually plex) have permissions for the entire path leading to those files (including the parent folders)?
unrelated: you might want to rethink the naming schema of your files / folders… this is pretty much set for failure at some point down the road.
Yes, e.g. the season folder should be named Season 01 instead of S01 and all the technical tidbits can cause Plex to stumble when attempting to match the files (if you absolutely depend on keeping those, best to put them in some square brackets […])