I think for the other things there's actually no special handling needed, because when the edited blueprint didn't include let's say trains, then no trains will be placed on the editing surface, so no trains will get saved into the new blueprint after editing. Same goes for entities, modules, tiles and even train fuels. If you want to remove any of those from a blueprint, you can just remove them from the editing surface, and they will no longer be part of the new blueprint.
The only thing that's different are the train stop names, since you can't place a train stop without giving it a name.
An idea how to handle this without creating some new GUI would be if the edited blueprint doesn't contain station names to just give the stations on the editing surface some placeholder name like "<UNNAMED>" or something like that when they are placed (either from the original blueprint, or when the player adds a new station). Then when creating the new blueprint check if the station name has been changed by the user, if so, then include station names in the new blueprint, otherwise don't.