[ BUILD # : 200808051401 ]
[ JDK VERSION : 1.6.0_04 ]

Here is what I did:

1. A project had references to old jars (x-3.0.jar) that had been
replaced (x-3.1.jar);
2. The project had three source roots with two independent
classpaths;
3. I tried to fix it by hand, doing a replace, since it would be (in
theory) much simpler than using GUI;
4. No other changes have been accidentally made, like breaking some
schema URL due to the replace operation;
5. When I save the file, the IDE hangs.