Symptoms - for those with a high folder count (>1000) on an external file share (e.g. SMB) media files are dropped during a scheduled scan.
The fix for me was adding the following parameters to my NSMB.CONF configuration file
dir_cache_off=yes
mc_on=no
The cause is still unknown. Those parameters affect directory caching. However, I’ve not found documentation that shows MacOS has any limits on those caches. Probably best to focus on how Plex deals with large numbers of folders in a directory and see if there are any limits there. If not then it may be a Sequoia problem.