Removing a web oder ejb module from an ear project does not work.
The application.xml file is not updated at all and the deployment fails.
(“Automatically update application.xml as needed” is selected for the ear project.)
I noticed that the .mymetadata file in the ear’s project root is updated correctly, but the .project file still references the removed project.
By the way, adding the removed module again to the ear is not possible, too. In “Remove or Add Module…” the removed module is not listed as “Current Module Project” of the ear and it is not listed in the list of addable projects (“New Application Module”).
Tested on MyEclipse Blue Edition Versions 6.5, 7M1, 7M2, 7.0