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If you have a Stereotype with the same *name* (but with different attributes) in two separate profiles, then when you edit an artifact, the attributes of the inactive profile are deleted. The solution would probably be to tag the stereotype with the profile to which it belongs.
This defect will involve modifying the artifact source and I really don't want to make any changes in this area. Users don't often switch between profiles and if they do, the chances of them defining the same stereotype name is even lower. If this is really needed, please reopen the defect and we'll figure out a solution.