Short answer is no, there's no easy way. Longer answer is to take a look at this issue:
https://github.com/wpilibsuite/EclipsePlugins/issues/15. If you change your HOME environment variable and then fix up things inside eclipse, you can do it. I'd suggest instead just keeping a backup of the ~/wpilib directory and swapping it as needed. If you also have two eclipse instances, each with a different version installed, you can just delete the ~/wpilib directory and then let them restore it.