This is just a guess: when you referenced one component, you created a link between the fragment and the main project. Now the linker will yell at you if it finds anything orphaned in that fragment. On the other hand, when you didn't link anything from the fragment to the project, the linker didn't bother getting involved because the entire fragment was excluded from the project. Maybe you could use ComponentGroup elements to round up all components and include them all at once?
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