I'm having a similar problem. I've got a Logic X (10.1) project file saved as a package. I have about 30 alternatives. When I do Project Management > Clean Up, many of the used files from the other alternatives are now deleted. What is also odd, Logic now asks me to download additional content (as if I deleted factory content).
This is from the manual...
According to my understanding, only files that are not used in ANY of the alternatives should be deleted.
Is this a bug or am I misunderstanding?
thanks!
Joe