I have 3 Pokemon on my Bench, and 1 of them has the "Omega Barrier" Ancient Trait. My opponent plays Cyrus {*}, and I choose to keep the 2 Pokemon that don't have "Omega Barrier". Does the Pokemon with "Omega Barrier" get shuffled into my deck?
Yes, it does. The effect of Cyrus {*} is on the player, not on the Pokemon with Omega Barrier.
Source: TPCi Rules Team (2018-05-31)
When using Cyrus{*} does my opponent shuffle in their Active Pokemon too?
No, your opponent only shuffles in their Benched Pokemon except for the 2 that were chosen.
Source: Ultra Prism FAQ (2018-01-19), TPCi Rules Team (2018-02-01)
The text on Cyrus{*} should say, "You can play this card only if your Active Pokémon is a {W} or {M} Pokémon". The original text says you can't play this card unless you have a {W} or {M} Pokémon in play, but the intended requirement is to have a {W} or {M} Pokémon as your Active Pokémon.
Source: Organized Play News (2018-01-24)