You must not have been at your home part when you upgraded, Or you relied on your own saved game and not the auto-generated home port save. This auto save is generated when you enter the home port office room after docking. Only the auto-save will load after an upgrade. This is not a bug. The reason this is here is because upgrades intensly modify the patrol game logic and data, so the game breaks when trying to resume play from inside a mission.
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