The "Edge 3D" Extension duplicates the selected Path object to create a clipping path. This mask is applied to a group of smaller paths that have a Gaussian Blur Effect. You can see this relationship clearly if you look at the XML Tree in Edit > XML Editor.
Unfortunately, this effect is not "live". Any changes to the original path are not applied to the "3D effect"-path. It would be easiest to delete the bevel effect and create a new one. If you really want to do it manually, you can edit a clipping path without unclipping by using the node-edit tool: