Old abilities remain in the data, just the references that point to them are changed to dummy them out (hence the 'greyed out/red slash' icons that replace them if they were still on your hotbar when they were 'removed').

This goes also for 'original' versions of abilities that were changed or updated extensively (such as class-specific abilities that became role abilities, such as Swiftcast or Rampart). The originals are still there in the game DATs, just dummied out and replaced by new abilities with similar functions and the same name.