We recommend uninstalling the old version of ermineJ before installing 3.x. You can retain your “data” directory and settings files, but making a backup is recommended in case you have to revert to version 2.x.
ErmineJ 3.x should still load old result files and settings, possibly with some problems. However, files from 3.x are not backwards compatible with 2.x.
The annotation, gene score, custom gene sets and GO file formats have not changed (though new formats are now available); your old files should still work.