Missions underwent an extensive overhaul. Many of the older missions may not be able to run.
The game installs (updates and whole game installer) do not remove anything from a users computer.
Only by uninstalling the game will anything be removed.
If a data path or folder changes, it could make any old stuff appear to be gone, but there is absolutely no code in any of our installers or updaters which will remove anything from a users computer.