Plex issue while adding content

I have a problem with my plex

After selecting the TV Show Folder all shows started to show up
Some 73 different TV Shows adds up in the dashboard during the scan
after a while during the scan I start to get messages “Deleted an Item on NAS” (NAS is the name of my WD mycloud EX2 Ultra).
During this also a Folder Named TVShows created on Plex Dashboard that contains some 600 Episodes which I do not have , It mixes all in one folder.
Screenshot of the event log

Searched Everywhere but did not found any solution for this.

Please show us some sample files/folders where your media is stored.

Folder structure is something like
I:\TVShows\2 Broke Girls\2.Broke.Girls.S01.720p.BluRay.x264-PSYCHD\2.broke.girls.s01e01.720p.bluray.x264-psychd.mkv (For Windows it is mounted drive)
/mnt/HD/HD_a2/2 Broke Girls/2.Broke.Girls.S01.720p.BluRay.x264-PSYCHD/2.broke.girls.s01e01.720p.bluray.x264-psychd.mkv(For NAS Setup)
I have tested 2 different installation Plex Installed on WD Ex2 Ultra and on my Windows .
Tested it via directly selecting the “TVShows” as root Folder during the Plex Setup.

Both time same thing is happening Plex Adds it then delete it , After waiting for a while there is only one Folder left named “TVShows” same as the root folder name. It contains some like 700-800 episodes all that files that are in Folder all in same.

You might give this a glance:

PLEX can be fussy about the folder structure and naming.

I would recommend removing the part highlighted in yellow below:

So change it from:

\TVShows\2 Broke Girls\2.Broke.Girls.S01.720p.BluRay.x264-PSYCHD\2.broke.girls.s01e01.720p.bluray.x264-psychd.mkv

to this:

\TVShows\2 Broke Girls\2.broke.girls.s01e01.720p.bluray.x264-psychd.mkv

or to follow the stated PLEX standard:

\TV Shows\2.broke.girls\Season 01\2.broke.girls - s01e01.mkv

I would try the one above, sure you’ll have to ditch all the extra info, but PLEX expects it a certain way. And while it may work fine (straying from the standard) for a while, any update could break it either now or in the future.

I wish I could do that .
The main reason of that type of Folder naming is for seeding purposes .
I tried harlinkin and softlinks both seems to works but it gets more complicated .
Problem with Hardlink it have to be same drive (Which I use NAS) Softlink is ok but I have to create manually for each file when the Sonarr is completed the download (as for Hardlinks).
I think Plex should be more simple as Kodi , Sonarr etc they get the files from respective folder in spite the name of the Season Folder being named as Torrent Folders.
I am ditching the idea for Plex because Seeding is more important than some fancy naming.