Do all New Game Plus - files merge?

I finished the Golden Deer route, then started a new game + with the blue lions. I now re-played the final mission of the golden deer route to also start a new game + to play chrimson flower. When I finish both routes, will the next new game + incorporate all weapon efficiency ranks for all students? So if I do the silver snow route, can I recruit Mercedes and Raphael and buy their ranks?

No, in order to transfer NG+ data between routes, you must first complete your existing NG+. Otherwise, the saves will not affect each other- choices made in your BL save will not affect your CF save, and vice versa. You can, however, transfer any amount of save data over by completing a single route at a time.