A slightly unusual problem, I have five extensions and one trunk set up on a Freepbx 13 system that I have been using for testing. Most trunks and extensions are on chan_sip
I adjusted the trunk so that “Match (Permit)” was set to 0.0.0.0/0 to allow any connections and then no extensions could register. As soon as I removed the entry all the extensions came back on line.
Any idea why the trunk settings would effect the extensions in that way.