Pretty much title. I used the Cloudquell potion during a fight with Nimrod (not the Agari boss, the one from the collector mini-quest). It reset the colour of the sky back to normal, but I believe I am still in The Cogah because I can see the remaining Agari bosses that I needed to fight.
#Using the Cloudquell while in "The Cogah" will reset the colour of the sky
humble violet
wintry folio
I've had this, I've also had that when doing a dungeon in cogah on leaving the dungeon the sky is normal again. But I still have the modifiers and bosses on map so still in cogah.