Nextcloud client deleted local files that it was supose to ignore

Hi @bb77 thanks for the response but I probably should describe my situation better.

I am using the NC desktop client to sync my local files and folder to the server.
After installing the desktop client I choose which folders to sync with the server.
When I chose a folder I can then uncheck any sub-folder that I do not wish to upload and sync with the server.
In my case, I have one sub-folder that is unchecked and therefore is not uploaded.
This has worked fine and as intended since last summer.
Now, a couple of days ago I noticed the one sub-folder that is unchecked is empty. I then check the server and see that the sub-folder which is unchecked is uploaded but with only 3GB of the content.
I do not know how and why, all of the sudden, the NC desktop client tried to upload the sub-folder which is unchecked.

In the image, it is the last folder which is the unchecked one that has lost its content. This setup/structure has been the same since I setup the NC desktop client