A quick first inspection

I'm trying to grab all the classes, methods that are involved in producing the bug. It seems to narrow down to these packages and classes:

package org.eclipse.wst.server.core.internal;
classes:
* ModulePublishInfo.java
Publish information for a specific module on a specific server.
/* Observed: This class could be the center of the investigation since it has the save() and saveResource() methods. */

package rg.eclipse.wst.server.ui.editor;
Classes:
* OverviewEditorPart.java
Server General Editor page. This class extend from ServerEditorPart.

* ServerEditorPart.java
Provide editor page with error messages which will be displayed on the status bar

package org.eclipse.wst.server.ui.internal;
classes:
* Messages.java
Translate messages. This class declares messages.