while we are deploying ear in websphere console, we observed that path is showing where the ear deploys.
I searched where this path comes from and found that websphere injects deployment.xml into ear file under META-INF folder and path mention in this file.
My doubt is that where this path comes into deployment.xml and if we are deploying a ear file which already contains deployment.xml, can I override it with default deployment.xml with existing websphere...???
All the stuff which exists under "META-INF/ibmconfig" inside your .EAR, is so called "enhancement", which makes "Enhanced EAR" (IBM terminology)
That enhancement is some instruction for WAS, prepared in RAD or other IDE, to apply some changes to server config during EAR deployment.
"Enhanced EAR" is considered a bad practice, as it (you observed it) makes funky stuff to server without your wish.
So, you can make the EAR un-enhanced, during deployment turn off check box "Process embedded configuration"