The upagrade missions are all set in the Fijords, so you're not going to be able to do them once you've reached FoV and are stuck in the city.
I just tried to start a FoV game, and my Rejuvenation 8 potion cost me 1*dragon nail, 3*earth root and 3*giseng. On my original game (fully upgraded) it was only 1*dragon nail, 2*earth root, 2*ginseng. So I'd say (at a guess) you have the first upgrade, but not the second.
The alchemist in the city also has the extra ingredient cost, but the skill trainer in the battle tower seems fully upgraded (can go to level 15).