This happens for everyone. We need wait. Could be solved with daily server restart. There was new launcher update, so obviously is going some work on server/client files.
Restart is done at 7am (or so, not 100% sure). And unless is told that saving works, any progress in MP is not saved. Tomorrow you can easily test this with move to next base log off and on, if you are on new base, all is ok.
Dunno what caused this issue, but fortunately this one is very rare. There also is not indicator for that. I can't compensate time needed for buy new ship, but can at least help restore income you had yesterday. ... expect some extra moneys today evening or tomorrow morning