A prime example is that very front top saucer light cover. It looks like it was a light in season one, but by season 2, it appears to pretty much have been covered over and opaqued as you don't see it anymore in top saucer shots. Do you put it back in as a light even though it might not have looked that way by the "final day of shooting"?
That controversial flat, round upper porthole was a big surprise to many of us when first "discovered" - I had never seen it on the film footage so naturally I thought that it was originally painted over. The porthole is shown in the Matt Jeffries three-view drawings which appeared circa 1966-1967
(the same drawings which showed the gridlines on top of the saucer only). It's location seems to imply that it was meant to be a third, upper, white "navigation light", complementing the red and green, plus and minus 90 degrees from each of them. Actually, it did not seem to exist on the model until the 3rd major modification. The only thing previously in that area where some line markings. There was a flashing white light nearby, but it extended from the very
front edge of the saucer during the 2nd major modification
(Pilot Episode).
I have carefully studied the look and location of that porthole from available photographs dated before and after all restorations and I reluctantly conclude that it
did originally exist on the model during filming in 1966-1967, but the key point is that
it was never lit. Once you memorize its location on the front upper saucer
(use the weathering marks as a reference), if you look very, very carefully at a good video image, I swear you can actually see it in some of the footage! Especially when they show the saucer from the top
("The Tholian Web") and in some third season episodes. Granted, it's very, very hard to see - since it is not lit, the clear porthole blends in to the surrounding color like a chameleon, but I would include it in any restoration (as long as it is unlit, and with clear plastic fill). It can be seen in some photos before the model was restored, but it cannot be seen in a photo taken when it was on display at a college campus in the early 70's.
But don't even try looking for it when viewing on YouTube! Watch only a high resolution version, on a good monitor.
I suspect that the porthole was backed with a light color (maybe even silver) before being filled in with plexiglas
(or whatever Datin use for the lit portholes) which is why it is so hard to see unlit.
By the way, I did a full about face on this - when I first heard about that forward upper porthole, I thought for sure that it was never on the model when at the studio. But it's amazing what you can find after being alerted visually - images that you've been looking at your whole life, and yet details you never realized were there. And there is also personal bias - I did not like that porthole - I was hoping that it was not there!
Now if we can only figure out what the tiny little red "laser turret" looked like on the lower saucer sensor dome . . . (another relatively new discovery - my first knowledge of it came from the Polar Lights 1/350 kit and instructions)