Same problem here. WordPress version 4.4.2.
In wp_blogs, site_id for each record was set to 0. In the wp_NNN_options table for each blog, home and siteurl were changed from ‘https://www.normaldomain.com/blogpath’ to ‘https://network.zero/blogpath’.
In both affected networks, only the primary blog remained unchanged. In the All Networks list, the networks showed as having only one site.
Even after fixing the wp_blogs table and the affected wp_NNN_options tables, the dashboard home for one of my networks still says “You have 1 site and NNN users” even though the All Networks list shows the correct number of sites for that network. The other network’s dashboard shows the correct number of sites. In case it matters, the one showing incorrect is the original network, site_id 1. The other is site_id 3.
Hopefully this can be fixed soon.
EDIT:
I see at https://github.com/stuttter/wp-multi-network/ that there is a 1.8.0 version of the plugin that “removed the network.zero placeholder” among other things.
Is that version safe to use?
Has it also fixed the larger issue of saving a network causing sites in other networks to become unassigned?
BTW, in 1.7.0 that issue appears to be related to reassign_sites_handler() in includes/classes/class-wp-ms-networks-admin.php “orphaning out” everything in $_POST[‘from’]. On the Edit Network page, the “from” list is populated with every site not in the current network.
