Problem with HTML Template pages breaking when they are moved in Manage Files

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Has anyone else seen this problem?

I moved some html files that were created from the Daylight HTML Template pages to a new folder​ in Manage Files and it broke the links to elements in the page.

We are not using the Shared Files area. Is anyone doing this and does that prevent the issue? What about anyone who has uploaded to their course area? Do you have any recommendations?