That is the way it has been for years and years and Plex has never ever expressed any interest in changing it at all.
Plex does not believe that requiring the Plex Dance to refresh the way files were detected is in any way a bug. They just believe it is the way it works and they are VERY unlikely to make any change in that.
At this point including logs of a scan where the problems begin is the only way you might get a resolution to your problems BUT, judging by the lack of any official response from Plex, it may be that they have placed your issue in the same file as many other issues from the past and that file is never opened by Plex.
@tom80H seems to have been the only Plex official to respond (Last response Oct 14) and his help, in this case, seems a bit lacking.
I can help no more as my expertise does not extend to the nuts and blots of Plex’s internal operation but, if this is so serious for you, then you might want to take a look at Emby as they handle matching and duplication quite a bit differently.
