My SA LP is still running 5.6, and I've noticed that the intelligence entries for a ship don't get updated when they are refit to a new class. Individual contacts are not moved to the proper entry on the Tactical Intelligence tab of the Intelligence and Foreign Relations window.
I.e., all the Federation's Moskva corvettes were refit to Moskva 31 corvettes, but were still listed under the Moskva entry.
I tried to rectify this by just deleting the class in the Tactical Intelligence after I had refit the last member, but that just made the label for all the contacts become blank, both ont he System map and in the event window. The ships were not redetected under the new class.
I managed to fix it by manually fiddling with the DB (had to re-add the ships to the AlienShips table and modify the ShipClass of the entry in the Contacts table for each one. However that did lose my "last contact" information for all of them, but I can live with this.