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I'm pretty certain the only way to purify Lugia is to fill all the chambers with compatible Pokemon. In otherwords, you pretty much need to purify all the others to do it.
Could be wrong though, I haven't bothered completing the game myself.
To purify Lugia, you need to have all of the "rooms" in the purify chamber up to max tempo. It doesn't matter if there are shadow Poke'mon still being purified, simply put Lugia in one of the empty rooms and it should come up with a message that something looks different about the Lugia....and after that, it should be purified.
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