Success!
The original partner, i think is not the template one. Template one has the ID=99, and i can see it on the admin list with our initial publisher account, which seems to be 102.
selecting categories with partner id showed the old categories i've created during my project, thats why i was surprised not seeing them in KMC.
I ran, kaltura-sphinx-reindex.sh as you said, and everything (categories, content, and the other invisible accounts) came back to life in KMC.
Many thanks