MultiSite: new Sites not showing up

It appears your sites are not under the same network, and you have network 1 and network 3. Normally this would never happen on an average multisite unless plugins are installed that can change this.

Yes 1 WordPress multisite instance can run multiple networks of blogs, you have accidentally stumbled onto this feature, wordpress.com being a primary user of it

Navigating and accessing the admin of the other sites, and clicking network admin should give you access to that network, and you will see those 2 sites listed there, but not the others.

If you want to merge them back together, changing the site_id in the blogs table will work. Remember to remove the new network from the sites table, but only after changing the blogs.

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