I've read conflicting stories over the years about whether TMP's FX elements were saved. It's debatable whether Paramount would have footed the bill to recomposite those shots where the matte lines are very visible.
I have noticed that in some early Next Generation episodes, a clean shot of the TMP Klingon battlecruiser was used. (Same angle and lighting as in the film, but new background.) This may have been totally replaced in the new HD versions though.