I recently moved a PYT toolbox from one machine to another - both machines have Windows 10 and ArcGIS Desktop 10.3.1, and while the new box has been used to run some ArcPy scripts from the command line, it hadn't been used with PYTs to this point. When connecting to the folder containing the PYT in ArcCatalog, the toolbox did not appear (although its metadata did as a standalone XML file).
Suspecting something was up with this particular PYT file, I right-clicked to create a new Python toolbox. The new toolbox appeared but upon refreshing it too disappeared, with the metadata XML left in its place. The same behaviour is reproducible in ArcMap. PYT files are shown with the proper icon in the Windows shell, so the file association seems to be fine.
Next I attempted to copy my PYT file into the "My Toolboxes" location through the Windows shell. Viewing My Toolboxes in the catalog window, the PYT file was visible and remained so (and could be run successfully). Likewise, the Space Time Pattern Mining Tools PYT toolbox in System Toolboxes is visible but when copied to any of the locations under Folder Connections will disappear.
Has anyone else run into anything similar and determined a cause or solution?