If you want to compare files with eXERD files,
select eXERD > Compare with Each Other on system menu.
run Compare with Each Other
Because of limitation of eclipse, you CANNOT compare a .exerd file with a .erdx(XML form). Open one of the files and save as the same format, and then you can compare the two.
For example, if there are "A.exerd" and "B.erdx", after saving "B.erdx" to "B.exerd", then you can compare two files.