The original TOS effects were included on the Blurays, the same could be done for TNG.
They were on film though. Remastering the TOS episodes would be remaster whole episode from film, then replace effects shots.
TNG would be recreate the episode from original recordings (hopefully all sorts of deleted scenes would turn up in the process) then recreate VFX shots. To include the original FX would mean upscaling that footage and inserting in the new HD master.