Categories vanishing

Sounds like an issue with Sphinx.
First, make sure your categories do appear in the DB, like so:

mysql> select full_name,status from category;

We expect to see the cats with status 2.
If you don't see them, they got erased somehow, which is not something the upgrade can do. In fact, it can only be done manually since the API, at worst, can only soft delete them [i.e, change their status in the category table].

However, my guess is you WILL see them, in which case, I recommend you reindex you Sphinx with:
/opt/kaltura/bin/kaltura-sphinx-reindex.sh

Also, do you have more than one Sphinx instance? if so, it is possible only one of the Sphinx nodes is unsynced, in which case, I'd start by disabling all sphinx nodes but one and check.