I just ran into a problem where my main FileMaker server went down and wouldn't restart in the middle of production. I shut off the main server and performed a failover to the standby server. Everything went very smoothly for my Desktop and iOS users, but none of the databases will open via webdirect or php. The main webdirect menu works (address/fmi/webd), but whenever you click on a database you immediately get a message that says 'Database not available'. A similar message is returned when trying to connect via php (by running a dbaccess.php script). I tried rebooting the server, but it didn't help.
(I run my FM servers on Mac Mini's with Yosemite)