After some more searching I found this in the eclipse bug site.
Steps To Reproduce:
- create a Dynamic Web Project and call it "Project1"
- copy and paste this project, in order to create another one which is a clone
of the first; in the "Paste" dialog, specifiy "Project2" as the name of the
target project (instead of "Copy of Project1")
OBSERVED BEHAVIOUR:
The context root of the target project is the same as the source project. This
could be a problem, but it can be easily updated in the project settings and/or
in the server editor (module tab).
However, even the module name is the same, while it's usually equal to the
project name. So, in Project2/.settings/org.eclipse.wst.common.component I find
the following:
This causes problems when deploying modules to the server. Moreover, the module
name can't be easily changed through the GUI from anywhere.
EXPECTED BEHAVIOUR:
The copy&paste operation should update the web module name to "Project2", just
like it happens when you rename a project.
WORKAROUND:
Make sure the module corresponding to the target project has not been added to
the server. Then, manually edit
Project2/.settings/org.eclipse.wst.common.component and change the deploy-name
attribute value of the wb-module element. Close and restart Eclipse (!!!) and
the new name will be taken. If you don't restart Eclipse, even if you edit
org.eclipse.wst.common.component from within Eclipse, WTP does not take the
change (it seems it's caching it somewhere in memory...).