Issue Once a layer from a layered image (PSD with multiple layers) is added to the shader tree, even if it is subsequently removed from the shader tree, that layer will persist even after the layered image is replaced with another one.
Steps to reproduce
Create 2 layered PSDs, could be simple 100x100 squares with identifiable differences, for example, one with red, white, and black layers, another with green, blue and yellow.
Load one of the images into the clips list using "Load layered image." In shader tree click on add layer > image map > use clips browser. Choose one of th layers.
Right click the layered image in the image list and choose "replace with layered image". Choose your second layered image.
Whatever layer you added to the shader tree will remain, and the corresponding layer in the second image won't be loaded. For example, if you added the 2nd of 3 layers from the first layered PSD to the shader tree, the second of however many layers in the second layered PSD won't be loaded and instead, the 2nd layer from the first image will remain. And this seems to be based on the order in which the layers were created, for example, if you rearrange or rename the layers in the second PSD, the second layer you had initially created will still fail to load upon a replace.
The "missing" layer from the second layered image won't even loaded if the scene is closed and reloaded. It only gets loaded if Modo is fully closed, restarted and the scene then reopened.
Workaround
Save scene, quit Modo completely, restart and reload scene.