Rightlick a model -> "Replace all occurrences" to replace all of the same selected models on the map to a different one.

Requires the duplicated models to be loaded at least once in the same session.

So if you are having a large Map, such as WdMadrigal, make sure to explore the Map once so that everything is getting loaded. This is just the way how the WorldEditor works and how it prevents loading all LNDs of the Map while not neccessary.