If a project is configured to store the dependencies in Eclipse format (".classpath" file) and two users change the classpath (e.g. user1 add library A, user2 add library B) and commit the changes into CVS, then the second user must first update the .classpath file (it is not up-to-date). The dialog "Files Merged With Conflict" appears and the user press the "Merge" button. Then he merge the changes and press "Save and Finish" in the dialog "All Changes Processed".
After that a dialog appears that a project file was changed and the user press "Reload Project".
Sometimes after that procedure the .classpath file has no library entries anymore. It doesn't contain the merge result.