C.E. Evans wrote:
If the Yorktown was severely crippled by the "whalesong probe," then she was out of commission for repairs. It's definitely plausible that most of her crew are either recovering from the ordeal, and/or have been reassigned elsewhere during its downtime. Eventually, the Yorktown becomes a quickly-patched up Constitution-class ship just sitting there in Spacedock awaiting a new crew and a new mission. Starfleet decides to rename the ship Enterprise-A and assign it to Kirk's command.
The main problem with this is the time issue. With all that was going on, it doesn't seem to me that Starfleet would've been able to salvage the Yorktown, tow her to spacedock, decommission, rebuild/refurbish, then make the decision to recomission all in the span of a few days. Not if it was that badly damaged. We are talking about government agencies and beaurecrats here, after all.
already mentioned, the time between the trial and the time the Enterprise-A was launched could have been more than a few days. Long enough for the Yorktown
to be recovered, somewhat repaired, and then renamed.