Hi, Vipin.
oxTrust (Gluu's web UI) regenerates those files each time any SAML TR is created or updated, or when its service is restarted. It utilizes Apache Velocity templates stored in ` /opt/gluu/jetty/identity/conf/shibboleth3/idp/`. If you need to modify them (what we strongly recommend against, unless you are sure that must be done), you need to edit those templates, but in a such way that it won't ruin the general logic of it. This implies some knowledge of Velocity engine.
Please note that free Community support doesn't cover such indepth subjects. Apache Velocity is a well-documented technology, in case you are not familiar with it yet.