Thank you for the bug report.
PHP fast CGI does not strickly follow fast CGI specification, it still writes standard error to the original stderr (file handle 3).
PHP's stderr is assigned to a anonymous pipe when it was started by LSWS, LSWS log every thing received from the pipe to the stderr log. So when LSWS restarts, new LSWS instance can not pick up the old pipe connection thus can not log output of stderr any more.
We are thinking about always restarting another set of PHP processes instead of reuse the old one when LSWS restarts. But the difficult part is when/how to stop those old PHP processes.