No i didnt trade them away, they were just not getting connected even though i had sailing for some reason. I couldnt replicate that behaviour when i started a new game.
IGE is just a ingame map editor, it doesnt actually modify any units, it lets you add units, etc to the map.
I did notice that if you add a resource to the map, connect it, then take the improvement or resource away (not pillage), the resource stays connected, but that might just be the game not knowing how to handle a resource dissapearing from a tile.