I thought the TOS remastering crossed the line a tad when they erased a statue that was part of the set in Wink of an Eye. Redoing a matte shot is one thing...
It would be really funny if the original TOS FX raw footage turned up someday. There were so many FX and optical houses involved, it was probably scattered to the winds after the show ended. One of the FX guys later worked on the horror classic Phantasm, and reused the transporter effect for when the mortuary dissolves at the end.