I actually have a fresh kit that I am building right now this is not an "early" kit problem. I know exactly what your talking about as I just ran into myself. From what I know the 90SE headblock is threaded but they supply the locknut for it anyway. Since it is threaded all you should need is some locktite on the 4x20 bolt with out the nut as this is what I did. Just make sure that it is tight.
As an option I have heard that people are using main rotor blade bolts for a Raptor 30/50V2 as replacements so that the supplied locknut can be used. Remember no loctite on the end of a screw with a locknut.
If you ask me it is complete stupid to include the locknut. I wonder how many people have been confused by this. You know how much money they would have saved by not including the locknut in every SE kit? It's the stupid things like this that frustrate people.