In case that configuration changes does not get written to disk in ISPConfig 3, you should enable the debugging mode.

Login to ISPConfig and go to:  System > Server config > Server (name of the server) > Server

and set Logelevl to Debug.

Old Versions:

If you use a ISPConfig version < 3.0.2, then debugging has to be enabled in the configuration file:

Edit the ISPConfig configuration file:

vi /usr/local/ispconfig/server/lib/config.inc.php

and change the line:

$conf["log_priority"] = 2;

to

$conf["log_priority"] = 0;

The debugging information can be viewed in the system log in the ispconfig monitor and the output is also logged to the file /var/log/ispconfig/ispconfig.log

If you run a multiserver system, then you will have to enable debugging on the slave were the error occurs and not on the master node.

How to enable verbose logging (debugging) in ISPConfig 3?
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