Graham,
Where the autoupdate on an aircraft is set to Y if you pick up that aircraft with you box and the local Navdata is different to the server data, the local Navdata will sync with the server contents. If however you have the aircraft set to N as you have amended some part of the data on your local database and also have unticked Auto Update Manually Changed Records in Preferences/Radarbox, when the aircraft is picked up the sync with the server will not be carried out.
The database update works in a similar manner but instead of a single aircraft that your box has picked up, deals with the entire database or not again dependent on what your N and Do Not Update Manually Changed records preferences are set too
Hope that helps.
Alan