I have never heard of this happening.
I've seen cases where a previous SDK and all customizations were wiped out because installed in the same location as the previous one, but never an install that installs the Eclipse IDE only.
Have you looked to see if the old directly is still there that you created previously?
Since you can get the IDE installed, try the instructions here which leverage the .7z raw files and bypass the installer: How to Import a New SDK into an Existing WICED Smart IDE
I'm thinking this may be the best path to get around this anomaly.