I've seen where a computer's NIC card patched into a digital station port on an expansion module would take down all phones on the digital module. (Also where they were cross connected to feed cables going to IDF's, and some pairs were shorted in the feed cables).

Label and disconnect ALL patch cords going into the expansion module, probably reboot, then connect a phone locally to test. Keep that test phone working as you reconnect the patch cables until you kill the module again, and you're probably found the wire run that is shorted or has a computer NIC plugged in at the far end