I can summarize the issue with the following picture:
For The Same Database "CL" when I login using OS authentication I cannot view the data, while if I login using the DB authentication I can view it !.
Everything was working fine before upgrading form 10.5.0 to 10.6.0. I used another machine that runs 10.5.0 with the same login info and it worked fine just to eliminate any permissions or privileges change issue.
I assumed that the issue from my machine so I went further and a upgraded a new machine but unfortunately I had the same issue !.
The same issue happen with me with I upgraded form 10.5.0 to 10.5.1 and here is the link for the post
Features inside the Enterprise Geodatabase not showing after upgrading to ArcGIS 10.5.1
Asrujit SenGupta provided the following links
ArcGIS 10.5.1 & ArcGIS Pro 2 bug connecting to sql server ?
ArcGIS 10.5.1 (Desktop, Engine, Server) SQL Server Permissions Patch
it seems that was a bug in 10.5.1 so installed the patch but it didnt solve the issue so I downgraded!.
Did anyone noticed the same behavior?
My recommendation will be to contact Esri Tech Support with a reproducible case and let them troubleshoot this.
Thank you Asrujit, I will reach them out today.