I've just done a test and managed to import a role that was controlling access to an entity present on the origin CRM but not present on the destination CRM. the import went though without errors. the role was created on the destination, but the role's
settings for the custom entity disappear. So, even if that may not break the system, it Can cause confusion. Specially if you are moving across DEV, TEAST and PROD systems. Not a good practice.
I Hope I could help. If I have answered please mark as 'Answer'. If was just helpful, please vote. Thanks and happy coding! Bruno Lucas, http://dynamicday.wordpress.com/