SMB folders do not show up

I am having a very strange problem with my kodi installation.

I am on Jarvis 16.1 x64 windows 8.1 (same happens with krypton 17.1 – tried it no difference whatsoever)

While all my TV shows did show up normally, from one point onwards (i do not know exactly when this started happening) they disappeared.
On further inspection i saw that Kodi was not seeing their folder, which was still there.

To be more specific
In my NAS my TV shows are as follows. I have an A-Z folder structure so lets say for T it is:

video\Series\Foreign\T\ The Name of the TV show

Now Kodi out of all the different shows in folder T sees only a portion.

But the folders are there. Windows have full access and they are full of files, the files that kodi itself was seeing some time ago.

it does not seem to be a network issue as the folders work fine. They are accessible through windows and other devices (they are not hidden)
Kodi can access each letter folder but it chooses to see only some of the shows in it.

I tried a clean install nothing.

I disabled the SQL database and attempted to build a local one, nothing as the problem persists even before scanning the sources because the folders are missing (only for Kodi).

I tried to change the names of the folders to reduce length, made no difference the folders that were missing in the new structure were still missing in the new shorter one.

I moved a TV show that Kod was not seeing to another location up one level, Kodi still showed the directories (one level up) without it

The same problem happens with a PC Share of TV shows (identical structure) so i know that it is not NAS related

I tried kodi installations from other pcs same problem.

Has anyone dealt with anything similar? is there something that can be done? I cannot understand why this is happening and it drives me crazy.

Update:
I attempted the following step by step
1. I copied the folder that kodi did not recognize to another location (external drive)
2. I created a new folder. Kodi recognized the “New Folder”
3. I renamed the new folder to the exactly same name of the TV show
4. Kodi recognized the folder with the TV show name without any content in it
5. I copied all the files from the external hard drive to the new folder that has the same nae
6. Kodi recognized the folder with the content no problem!!!!!!!

What is the problem, some folder attributeConfused I am baffled. I will have to do this process by hand for all shows.!!!!