I tend to work with many workspaces, creating each for specific needs. I use the File | Export | General | Preferences to export my preferences into a file. Then in the new workspace I use File | Import | General | Preferences and load up the preferences file.
The only time I have any issues with this is when I move thep references file to a different computer which has different JVMs installed, or JVMs installed in different locations. But when that happens the only thing I have ot change is the registered JREs in the preferences - everything else in imported without issue.