Eclipse is quite self contained and the launcher seems to work well even when Eclipse restarts (Task Manager shows it's still running, ie didn't start cleaning up)
The update released via the updater to the main Eclipse are mostly bug fix only, meaning no portability breaking changes should be introduced and most of the Official plugins on Eclipse's site are portable as in saving settings only in the workspace and the main Eclipse dir.
The only exception is if a plugin decides to store stuff outside of the workspace or if the plugin uses an Eclipse feature that saves stuff outside of the workspace the gluxon didn't portabilize. (Like the secure storage for example)