I've never believed for a minute that the Enterprise-A and the Yorktown were the same vessel. Star Trek V gives every indication that the Ent-A is a brand-new ship.
The only reason why this debate even exists is because of the Ent-A's decommissioning at the end of Star Trek VI, and why Starfleet would decommission a seemingly brand-new ship after only a few years of service. But there are in fact several reasons:
1. The ship was faulty from the start. If the vessel was found to have a major design flaw after a certain period of time, that would justify a quick decommission.
2. Starfleet's attitude was clearly that the Excelsior class was where it's at, and older vessels could have been decommissioned to be broken up for raw material to build the new ships.
3. Starfleet already had the Enterprise-B under construction and wanted to decommission the older vessel before the new one was completed.
4. To go along with #3, Starfleet could also have recommissioned the Ent-A with another name so as not to step on the toes of its newer namesake, and to still be able to utilize a relatively new ship for some other duty. To me, this seems the most logical idea of what happened to the Ent-A after STVI.