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I'm not sure what Cat6E actually is, I only know of Cat5E and 6A. Either way, you don't need all cables for it to work.

Only four out of 8 conductors are used for anything up to 100mbps ethernet. For 1000mbps (1 gigabit) and 10Gigabit, you need all 8. 10/100mbps only needs pin 1,2,3,6. However, autonegotiation of the devices means you might have to set devices at both ends to 100mbps manually if both are gigabit capable (they're not always good at detecting cable capabilities).

I don't think there are any gigabit capable Sky boxes so you should be fine.