if you installed unmanaged on the top of a managed, you make the change permanent
http://msdn.microsoft.com/en-us/library/gg327822.aspx
if you allows customization over it and someone add a dependency, you have no choice but delete the dependency
this may cause problems also:
http://stackoverflow.com/questions/14197111/crm-2011-unmanaged-changes-to-managed-solution-form-gotcha
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/