Okay, legacy web application - what appserver? Seems like the bug here is that, if NetBeans is starting the application server, that it should detect (from configuration files or wherever) the encoding that application server will use for logging (or know what it is). That would be an actual fix without interfering with anything else.
Failing to detect or know output encoding from an application server is the actual bug here. In the meantime, you could either keep your netbeans.conf setting, *or* set the system property file.encoding to your system default in your appserver's configuration to be consistent with NetBeans' expectations. -Tim
