The default for Purge Unused is currently set to Check All, this makes it too easy to purge a lot of stuff that will still be needed as a project is developed. Most of the time Purge Unused is used to get rid of the needless duplicate families Revit makes of stuff brought into a project, and only at the end of a project if the model is sent to another firm would Purge Unused be set to to Check All.
Check All should be an option and Check None should be the default.