I was under the impression that the filming model, which I understand is the one at the Smithsonian, arrived with the three tone paint scheme but was repainted two-tone (or did it arrive two-tone and end up being repainted three-tone?).
According to Scott "Captain Cardboard" Alexandar, when AMT delivered the original miniature(s) to Paramount they were painted a single shade of medium grey. Matt Jefferies added the green prior to filming. The confirmation that the two-tone paint scheme actually went before the cameras came from the late Robert Justman.
1968: Because it was anticipated that both AMT miniatures would eventually go before the camera they were each given identical paint schemes. Alas, only one D-7 was ever shot, and that model was given to Jefferies after the show wrapped. The other identically painted model went to Roddenberry. To this day there is debate over whether there were actually two shades of green used on the model (as opposed to a single shade).
1974 (approx): Matt Jefferies donates his D-7 to NASM.
1976 (approx): Paramount "borrows" the Jefferies D-7 from NASM for use on Phase 2. While at Paramount the model is
completely re-painted and disassembled. At some point the determination is made that a larger Klingon miniature is needed, after which time the model winds up with Ed Miarecki for restoration. Unfortunately, Ed didn't have proper reference data of the model's original appearance, hence the inaccurate paint scheme in evidence upon its return to the Smithsonian.
This is by no means the last word on the subject... simply a well-informed account from someone I know pretty well and have found to be consistently reliable.
In addition, here's what Jim Key's Custom Replicas D-7 instruction guide has to say about the D-7 paint scheme…
As you can see, there’s a
lot of latitude here for individual interpretation.