The layer tree has limited functionality when a floating/detached layer or model tree is used.
When creating copy geometry features from other parts, the user must select geometry in the popup graphics window. If the geometry is hidden you can select the layer tree option and the layer tree will split into two sections: one for the target model and another for the originating model from where the original geometry can be unhidden. However, if the user has the option for a floating model or layer tree, the layer tree will not split into two sections to allow them to unhide layers and the copy geometry feature must be aborted.
Use both a floating model tree and a floating layer tree and add the layers button to the quick access toolbar. When selecting geometry for the copy geom feature, click the layers button and a new layer tree will pop up for the originating model. This does not work when the model tree is detached and the layer tree is attached. Another workaround is to open the originating part and unhide the geometry to be referenced and then re-execute the copy geometry feature in the target model.