After inspecting the Murkrow's nest area for loot I over hear the one called Less inquire about a cure to the conditioning of shadowing.
"As far as I'm aware, the painstakingly long process of fighting with a shadowed pokemon will eventually bring it back to normal provided it doesn't go into a rage and...well... you saw what the ONE bird did to what was it..... FIVE of our pokemon.... Just wipe them all out in one hit... So, now I believe when they become healed, they too will be infected with the shadowing...disease? Ahm, there is also the possibility that you find one of these," I say pulling the Time Flute from my backpack, "It's called a Time Flute and it has the chance to cleanse a pokemon of it's shadowing in one go provided it listens to the music that soothes the savage soul. However this item appears to deteriorate upon usage, I'd say this one has maybe three more uses left before it's completely broken. I'm unaware of a means to repair it. That's roughly the extent on my knowledge of shadowing."