The Burned Tower's static Entei encounter data was removed entirely.Staryu's holdover egg move data was removed entirely.The Safari Zone and the Haunted House attic were also affected by respective blockset changes, but to a much less severe extent.
As for the Mahogany Town and Route 45 unseen messages, they were both changed, as seen in the unused text subpage. All the unused data from Gold and Silver remains in the code of Crystal, virtually all of it unchanged aside from a few exceptions, which are documented below:
