If you use the Replace Links feature to replace a BOM texture, the "new" texture is placed at the top of the list. Because list order is essential to the proper baking of textures, especially body and head textures, this causes every outfit to failure to bake correctly.
Having searched for a global way to reorder textures (and finding none, not surprisingly) this places the user in the unenviable position of individually manually editing potentially hundreds of outfits.