Okay, I'll weigh in on this, but understand that I'm not attempting to supply excuses for anyone involved... just context. There were any number of points at which the fate of the 33 inch Enterprise might have turned out differently, maybe to the point that we'd be celebrating the 50th with two Enterprise models rather than just one.
What role did the 33 inch model play in Star Trek II (Phase II)?
The original concept behind the Phase II Enterprise was that it was to look like the original Enterprise having been upgraded with some new parts, but was mostly the same as seen in the original series. Jefferies was using the 33 inch model as a reference as it was one floor down from his office in Roddenberry's office (the 11 foot model was already at the Smithsonian by this time). As Jefferies became pressed for time (he was working full time as the art director for
Little House on the Prairie) he started omitting details from his plans for the studio model that were to be essentially directly transferred from the 33 inch model. This included the color (which Jim Dow had confirmed recently complaining about the Phase II Enterprise model being a greenish gray), hull markings and window placement.
I don't believe the model left Roddenberry's office for any of this.
Why was it loaned to Robert Abel and Associates?
While Richard Taylor pushed to redesign the Enterprise from scratch, Roddenberry insisted on using Jefferies Phase II Enterprise as a starting point. Roddenberry liked this general design far more than any of the
concept designs put forward by Joe Jennings and Mike Minor, and he really didn't want to go through that process again. Because Jefferies plans required the 33 inch Enterprise to fill in some of the details, I'm sure he believe that giving over Jefferies plans to Richard Taylor's team included the model.
Richard Taylor really didn't like listening to Roddenberry to begin with and most likely never understood the connection between the Phase II Enterprise plans and the 33 inch model. Further, not being a fan of the original series, he most likely never knew what he had was the first model of the Enterprise. Add to that the fact that he really thought that anything having to do with the Star Trek II series should have been scrapped (his words) and it isn't hard to figure out the fate of the model (she wasn't exactly in friendly territory at this point).
So there was a brake down in communication (and it was an on going problem, so it wasn't unique to this issue).
Severing ties
So the team from Robert Abel and Associates was falling further and further behind schedule and had eaten up a ton of money, but hadn't really produced any useable footage. Richard Taylor's team was let go and a new team headed by Douglas Trumbull came in to save the film.
Sure, this would have been a great time to ask for the model back... but considering all the other pressures Roddenberry was facing at that time trying to get TMP to theaters, it most likely slipped his mind.
Missing in action
Star Trek: The Motion Picture made it to screens in December of 1979 and within a few months life started to get back to normal. This is when Roddenberry noticed the absence of the model from his desk and called Bob Abel to get it back. Abel was unable to find the model and informed Roddenberry of this.
Why the mystery?
Honestly... I think Roddenberry didn't want to damage any possible future dealings with Robert Abel and Associates, so it was easier to leave it at
it was loaned out and never returned and
he didn't recall to whom it had been loaned.
An additional note... yeah, this was less than 10 years after the original series, so a lot of these models weren't seen in the same light as today. Greg Jein was hired to build the Klingon battlecruiser models for Star Trek II and the Smithsonian loaned him the original (first) Klingon studio model. He broke it up, made molds of all the parts and returned the pieces in a box to the Smithsonian.
That wouldn't happen today.
On the use of the 33 inch model, besides being used in every episode during the opening titles, it also appeared in the following...
The Cage
Where No Man Has Gone Before
Charlie X
Tomorrow is Yesterday
The Deadly Years
Obsession
By Any Other Name
The Enterprise Incident
Is There in Truth No Beauty?
Day of the Dove
That Which Survives
Requiem for Methuselah
It also has the distinction of being the first model of the Enterprise to be shot (December 1964) and the last model to be shot (December 1968) during the original series.
I put together a short history of the model
here, though it could use updating. And I've made some good progress on replicating the model, here are a few progress images...
I've got a long ways to go, but it is cool seeing it sitting there (when I have it assembled).
Edit...
Oh, and here are some reference shots of the 33 inch Enterprise...
And how my study models and current studio scale replica compare to the original...