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Interesting conundrum: In Untold Voyages #5, the Yorktown is still in the configuration of a TOS starship, and is said to be bound for decommission (in 2278).

The TOS-configured Yorktown reappears in the novel Crossover, mentioned to have been a museum ship for years (by the late 24th century).

The Star Trek IV Yorktown is never shown, but the STTNG Technical Manual mentions the Yorktown was renamed Enterprise-A .. should the ST4 reference be moved to the Enterprise-A article? Or possibly the ST4 appearance was the crew aboard the decommissioned museum ship, and at the end of the film the 1701-A is a new Yorktown, renamed? -- Captain MKB 23:46, 8 March 2008 (UTC)

Definitely an interesting conundrum. FASA seems to support the idea from the comic, that the Yorktown was never refitted beyond Mk III Constitution-class specifications (Achernar?), and lists it as being scrapped in 2211 SFC (mid-2270s). This would then work with the Yorktown being preserved as a museum ship with original Connie specifications into the 2370s. The reference to the Yorktown being refitted in TOS short story: "Night Whispers" (2273) could just be some minor equipment upgrades without the external specifications being touched (NOTE: Have to check that reference).
The one problem, however, would be the Yorktown in ST IV and beyond. Now we could assume that Starfleet decided not to decommission the Yorktown and simply refitted her, and only decided to rename her as the Enterprise-A at the end of the film. Captain Randolph could simply be commanding the Yorktown on a shakedown cruise before the Probe hit.
Unfortunately, FASA and Mr. Scott's Guide to the Enterprise states that either the USS Atlantis or the USS Ti-Ho were renamed Enterprise instead. --The Doctor 00:31, 9 March 2008 (UTC)
Its possible the ST4 guys were simply crewing the old decommissioned Yorktown on some sort of USO tour when it was disabled, and as to the new one -- if the 1701-A had three names before being given to Kirk, its no wonder they might've been happy to dump all those names and settle on a good one. -- Captain MKB 06:38, 9 March 2008 (UTC)

An interesting development in checking the reference from "Night Whispers". The Yorktown was a new ship which was in the early stages of construction at the San Francisco Fleet Yards in 2273. This means that we could be looking at two Yorktown's, the first Yorktown being decommissioned in the mid-2270s (per the comic and FASA) once contruction of the new Yorktown was completed. This could indicate that the new Yorktown the ship seen at the beginning of the film, was brought into Spacedock for repairs and renamed Enterprise. --The Doctor 10:21, 9 March 2008 (UTC)

(all possible, but I should point out no Yorktown was actually "seen" in ST4, just mentioned during a communication with the ship's captain)
this could mean the Yorktown was constructed over a long period of time -- the 2273 construction wouldn't have been complete until after the 2278 original left service. in that case, it is possible the ship was officially named Yorktown only after the original ship went to museum, but still had a planned name while in its early stages (possibly Atlantis and Ti-Ho were early drafts?). -- Captain MKB 14:35, 9 March 2008 (UTC)