Could JBDS provide a functionality that could synchronize the source and deployment in a two way manner. That is, if any change made at the server side after deploying could be pushed back to the source in the JBDS IDE.

It seems that currently IBM RSA IDE has such feature with IBM WebSphere server. Please check the attached ibm_rsa.png for more details.

Eclipse also could workaround this with Tomcat server by setting the "working directory" as the project workspace location something like ${workspace_loc:Project}. Please check the attached eclipse.png for more details. It doesn't seem that there's any additional functionality at server side that pushes the changes back to eclipse project. It's just a matter of setting eclipse working directory as the project source path. However, the JBDS doesn't seem to allow user to set the "Working directory" in this way.