Variables only pulling from single collection

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In our library we have 3 colour libraries:
 

• primitives (color scales)
• semantic
• component

We have linked our primitives to our semantic and in general the semantic ones to the components which works fine when testing light mode dark mode etc. 

Some instances we need to pull from the primitives into the component collection, but this just doesn’t seem to work. 

Any one know why? what might we have done wrong?