SafeMode file loading (holding L+R for 10 seconds on a save slot) will now always teleport the player to the orphanage.The 4 destroyed maps now also contain the Greater Drake sidequests. Not only does it make capturing those drakes impossible, but it also prevents the player from using Eliza's duplication feature to find legendaries in the wild (including the Abyssal Tyrants).
If the player triggers the Abyssal post-game content, Greater Drake sidequests in the skeleton maps are lost as the maps are destroyed.