The F being decommissioned has something to do with a fault in its computer system according to those Instagram logs. Not because of its age.
My head canon reason is that, rather than refit the computer system, Starfleet completed the several ships of that size in the 2380s as kind of a "sunk cost" follow up to the Galaxy-Intrepid lineage that migrated in some Sovereign tech, but as part of the lessons learned review from the Dominion War decided that it was the 23rd century mid-sized "modular built" ships that allowed them to have a large, sustainable fleet. Therefore in the 2390s they shifted back to mid-sized ships (still larger than most 23rd century ships) that shared common parts in different configurations.
There is real world precedent for this. The US Navy's Zumwalt class of destroyer is the largest ever built and was supposed to see 30 ships. But they were too big, too hard to build, and too much of a technological outlier, so they curtailed it to 3 ships, and resumed upgraded versions of it's predecessor class. The next class will take the Zumwalt tech, modernized, and put it in an easier-to-build hull.
The Connie-III, Sagan, Duderstadt, Echelon and maybe the Excelsior II all share common parts. Even with Replicators, building starships still takes substantial work hours, and through real world modular construction you could build a lot of those classes of ships by combining independently built parts, in the time it would take you to build a single Enterprise-F type inside-out. And on top of that, upgrades you make to "Connie-III, Sagan, Duderstadt, Echelon" "family of classes" couple probably be applied to all of them, whereas it would need modification to be back integrated into older ships of unique designs.
This is, incidentally, something the US Navy is going through right now because it wants to get rid of all the 1980s Los Angeles-class subs ASAP, despite some of them having years of life left, to go to an all-Virginia-class fleet because it'll take less work and be faster, to support one large attack sub class, and not two (putting the 3 class special mission Seawolfs aside).
Again this is all head canon, but applying real world reasoning to the seeming early retirement of the Enterprise-F has it make all the sense in the world. It would be incidentally the same reason that the Galaxy class is gone. But in keeping the Sovereigns an the "Battle of Sector 001" era ships around, despite their more integrated designs than the 2390s/2400 designs, they too share a common set of technologies. Galaxy/Nebula and Enterprise-F type really seem like outliers.