Refactoring->move/rename on classes does not seem to alter the affected config files. Here is a case to reproduce the problem
I have a webapp, created a servlet, the servlet entry was added to the web.xml correctly, now I did a refactor->move of the servlet into a different package and voila, the new path was not changed in the web.xml.
I assume it is the same with the hibernate config files.
The MyEclipse version I use is 3.8.4 on 3.1m7 but I assume it is the same on eclipse 3.0.