Say I have 2 collections, each is rooted at CustomerEntity and each has been joined to a context. Collection 1 has a prefetch of Customer - Orders and Collection 2 has a prefetch of Customer Employees. Each has fetched customer 1,2 and 3.

Because of the uniqueing actions of the context. After I fetch into collection 1 and collection 2 customers 1,2,3;

I expect that the customer entities contained in each collection have been made unique and that each customer entity has both it's OrderCollection and it's Employee collection filled.

Are my expectations correct?

Yes, your expectations are correct Remember to add the collections to the Context before fetching collections.

(Ref: LLBLGenPro Help - Using generated code - Adapter - Using the context - Prefetch Path fetches)

Thanks