After leaving Dungeon Freedom in SI, you have to collect your companions throughout Moonshade. Dupre can be found at the Blue Boar Tavern, except when I find him, he's sitting in mid-air, and not using a chair. This is with the latest SI Fixes and Exult versions.
Attached is the best savegame. Simply walk to the Blue Boar Inn and you'll find him.
Confirmed with bth SI fixes and unmodded SI. In the originalDupre sits at the table next to the entrance.
How did this get fixed? His location was assigned by Usecode, so I was looking at fixing this in a mod.
At the start of the Waiter_schedule, we now check to make sure the NPC is sitting at a valid spot (on a chair by a table). If not, we find one and have him walk there.