Up to now, the “Replace” layer can only change tile layers (Ground, Objects, Above and Walkable) but no object layers (Mapevents, Spawn, Key and Replace).
To change any tile layer, you have to create one new layer for every single layer you want to replace with other tiles and give it a custom name. The new layer should be always on top of the layer you want to modify. You can raise or lower the layers by right clicking the layer window. Only redraw the tiles in the selection box and leave the rest of the layer blank.
To delete several layers, you can create one new layer for all these layers and leave it blank.