To save supermarks, navigation fixes and crew messages you need to 'save journal'. It's the icon on the right below the Captain's Log. Enter a name in the journal dialogue and hit accept.
Then, each time you relaod a save you must reload the journal, it will not load automatically.
Note that placing supermarks is somewhat tricky: you need to zoom out first on the map to place them, after that you can zoom in and move them accurately to the desired position.
Only the above will be saved, normal marks, protactor lines, circles etc. will disappear when you leave session.
Cheers,
XS
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