The herb and branch only show up beside the talking tree when you have the respective quests (you need the branch for Corinna's summoning quest in Verdistis). With the world file replaced, the herb that was placed on the ground got removed. You can get a replacement herb (it may be a silly quest, but the alchemist will teach you a level of Alchemy for it);

Lost Items - guide and directory of inventory files


There are a couple ways to bypass the re-sealed door in the thieves' guild, or you can use the fix above to get the holy dagger;

FIX for the Missing Catacombs Portal
or
Teleporting Anywhere, via hex editor