The game always crashes when the “my games/GSB/ships” contains ship setups created for a race which was removed when un-modding the game. The game could simply ignore the files,its not like they change anything there…
This could possibly happen also with scenarios/deployments,i havent tested that.
Earlier i also said that there is a problem with the game crashing when a race is selected that was removed (removing a mod for example). Again, the game could simply autoswitch to federation,which is a default unlocked race available even in the demo. - i also havent tested that so dont kill me for ranting plz 
just pointing out some really annoying loopholes