Update Has Destroyed My Trade Route

I've had this happen before the 1.3 update, so it's nothing new. A station in I Carinae used to buy Imp Slaves as it was controlled by an Empire faction in an independent system. System became Federal and Imp Slaves were outlawed. RIP one nice little trade route.

But whilst one trade route closes another opens up somewhere else. Time to move on to pasture new.
 
What I want to know is if a power is independent wouldn't it flip all the systems it owns to be independent? Why would federal and imperials own systems?
 
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