I am also experiencing the same issue with ArcGIS Pro 2.0 and seems to be a refresh problem with the system toolbox pane. One workaround I discovered is forcing a refresh by adding an empty python toolbox inside the product's ArcToolbox directory. To do this I created a new toolbox in ArcPro using Insert -> Toolbox -> New Python Toolbox and gave it a name that doesn't conflict with an existing toolbox. I then copied my new toolbox file to <arcpro-install>/Resources/ArcToolBox/Toolboxes. The next time I start ArcPro it will find the new toolbox file and force a refresh of the system toolbox pane. Then it will look for toolboxes in your site-packages/<package>/esri folders and display them. Once they are displayed the same problem will exist if you remove your toolbox file in site-packages/<package>/esri folder. The underlying toolbox will be gone but it will still display in the Toolboxes pane and throw an error if you try to open it. Another option is to store your python toolbox in a project template file and distribute the project template to other users or through your portal. Then, instead of creating a new blank project, you can create a new project from the template and your toolbox will already be loaded in the project. I'm still confused though with what is the preferred way since these two methods could conflict with each other where it's easy to load two tools with the same name and alias.
... View more