Sg335man

Hello, I was rather surprised when straightening my neck on my 89 reissue of a 60s 335 Dot, for fret crowning. After moving the wrench 1/4 turn I found the Trust Rod Nut and part the thread of the rod filed down catching the Rod threads? Several Luther’s have since told me this was common practice at the factory to fit the cover?? The angle of the neck being the problem? It just about works but you pay thousands for that kind of work? Thanks guess I will try another but and see?