If your media files are located on some kind of NAS or network file share, go back to the previous Plex server version: Plex Media Server support ending for older versions of Windows (7, 8, and 8.1), macOS (10.11, 10.12) - #4 by MovieFan.Plex
Yes, Plex has support for flac, provided these files are properly organized and tagged: https://support.plex.tv/articles/200265296-adding-music-media-from-folders/
With a collection like yours, I recommend disabling all the analysis features of Plex until the initial library import has been finished. Otherwise you may be waiting forever for the import to finish, because all the analysis processes are taking so much time.
https://support.plex.tv/articles/200289526-library/
