Retconning I guess - a number of the Deity Stones are now in different locations from where they were in 1.0.

As some of the original locations are no longer accessible/no longer exist, I guess SE decided to switch locations around for them just to have all of them accessible from the start, as only 1.0 players would actually notice the difference (lets face it, 1.0 players are a drop in the ocean in FFXIV's current population).