Well, quite. What would happen ?
I guess the feeder relationship between the two clubs would have to be terminated for however long they occupy the same division. Orient would then have to find another PL club to pair up with, or make do with whoever they've got on their own books.
Horrible idea. It puts a formal glass ceiling on the feeder club, as they will never be allowed to rise to the level of their "owning" club. And the feeder club would completely lose its own identity.
In the exaple the OP gives, if Orient were formalised as West Hams feeder club, and they made...