Does the ArcGIS Pro project actually cache toolboxes and tools that it may have "visited" in the "Project" file manager tab? In theory it is pointing to the same folder, toolbar, and tools that I can see in Window File Explorer and ArcCatalog. In Catalog, I have deleted the tools and in File Explorer, the .py files have been deleted. Even though Pro has been close (saved) and reopened, and it appears they are pointing to the same folders, they still are showing in Pro....and I can still run them.
The .py files do not appear of the drive....and yet Pro still sees them. Refresh does not work, so I can only assume they are actually copied and saved with the project. I can see this becoming a real bloat on the project....another reason why we still need Add Stand Alone Data Catalog Like ArcCatalog to ArcGIS Pro
I of course do not want Pro to auto delete things, (unless I do it), but a "rescan drive" or "clear cache" is needed to get this all back in sync.
This is related to (I have already looked at the suggestions) how to refresh file paths in Pro
BTW - Using ArcGIS Pro 1.4.1 (latest released version). I am testing using/updating my custom Toolbox\tools to work in both Desktop and Pro.
EDIT: Adding pics to help show the issue. All are looking at the same path. .py files and tools in .tbx were deleted using ArcCatalog .... after the folder/toolbox had been viewed once (or twice) in Pro....but even those tools that have been deleted (including the .py) that were never run in Pro yet can start up the gui for user input (although it will fail with missing script error). I would like the list of tools to be refreshed in Pro, if they have been physically removed from the toolbox.
....this may require a tech support call.