I actually noticed this last week. Got 2 collectibles from Spire, 2 from Ghost, but last week 3 of them disappeared, leaving only "first collectible in Ghosts" checked off... I logged off & then eventually logged back in & they were all magically all there again... Today, logged in & the same 3 went missing again... didnt bother doing collectibles for Prophecy yet, figure its a waste of time if they're just gonna disappear. Will probably have to run all three dungeons in the final week, may as well wait till then & do them all at once if we end up having to re-collect them.