Store your vehicles in the garage before you save and quit the mission. This will ensure they are all kept in the condition you left them in. IIRC the mission is designed to have only one vehicle stay spawned around your base between game sessions, so store them all instead of leaving them parked around the place.

Members of your personal squad will not persist between game sessions either. To ensure you do not waste resources (HR and $$), you can transfer the AI under your command to be a garrison. They persist between sessions so if you transfer them to a garrison before saving, they'll still be there when you load back in.

oh ok makes sense thanks

Oh, just one little note about saving your AI subordinates as a garrison between game sessions: It's worth noting their loadouts as a garrison will NOT be saved after loading a game. When you load into the saved game they will spawn with randomly generated equipment based on what you have currently unlocked at that time.