There is a SMB bug in the MacOS. It causes files to randomly appear as unavailable in Plex libraries. See this post for workarounds: Plex Files Unavailable but they’re not missing - #638 by Bat_Mang
Also check for database corruption. This is unlikely, since you deleted the existing files and started over, but it does not hurt to check.
Pull the server log files. Look in Plex Media Server.log, and rollovers .1.log to .5.log, for ERROR entries that say the database is malformed or corrupt (search for those terms).
If the database is damaged, use the DBRepair for Plex Media Server tool. Alternately, you can follow the Plex support article to repair a corrupt database.
