2= Use less objects (Depends on the object) because when they break they leave small bits rolling around the map, witch affects performance
3= Yes they will stay there, you might want to change the objects to visuals because some of the objects may block pathing even when they are in air. Same applies to bridges, you can't have a bridge you can cross and go under aswell. (The map is 2d basically)
4= I assume you mean water, well really its just what looks good and you prefer
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5= You probably mean backups, yes there is a slight possibility of corrupting the file. (i had it happen once) You can save the file by exporting it to the game and if the editable file corrupts, then you can use a program to extract the file back from the game. (Just copying the folder works just as good, but exporting is a bit faster)