Currently, about once a week for each app that require a manual download I do the following:
From the Intune Apps tab, Right click on the application and open properties.
Click Download URL. If I get a message telling me that the file has been found in the local content I move onto the next app.
If I get a message telling me that the file can't be found, I go to the vendor website and download the new version so that Patch My PC can update it.
It would be good to easily identify these rather than having to do manually check each app.
As another approach to working with the local content repository, I recommend configuring the Alerts tab if you haven't already.
When the Publisher syncs, it will send an email or Teams channel notification informing you it couldn't find the content in the local content repository for the new version.
How Publishing Alerts Work in Patch My PC’s Publisher