So I think recently (March 2018) Spotify changed it's decoders, those are being used to identify local files and import to it's library. The version I'm using is 188.8.131.528.g758ebd78.
I had some old mp3 or m4a files, mostly self ripped CDs in my local library, and I used Spotify's sync feature to my mobile device. But, since last update of Spotify (Desktop Player, in Windows 10) those files are gone, they don't even appear in "Local Files" section. Although they're physically present in the destination folder, Spotify removed it from it's list.
First I removed the folder from sources dir, and re-added, then turned off completely, but not good.
I looked it upon the support forums, there were some answeres related to "Install QuickTime for m4a support" and "use ffmpeg with movflags option".
So I decided to reencode my good old m4a files (and some old mp3s) into mp3. Re-encoding mp3 also helped, it cleared out some erroneous parts. And viola, all of them was successfully imported back into Spotify, automatically.
The command I used is;
ffmpeg -i "Artist - song.m4a" -acodec libmp3lame -ab 128k "Artist - song.mp3"
Hope it helps.