I don't know if the IR ports on the Harmony hub are addressable but if they are then your idea should work, provide there is no IR optical path from one Sky box to the other.

A more complex solution would be to use the SPC4 product

[Link: tvlink.co.uk]

But it would require a single IR emitter on a TVLink external IR receiver to control both Sky boxes and you would need to learn the new IR codes used by the SPC4.

The use of an IR emitter for a Sky box can be avoided with a wired IR input device such the as the KWE [Link: keene.co.uk]