New answers tagged document-set
Something about making these document library out of templates caused SharePoint to think the Document Sets were folders. My solution was to get an intern to painstakingly recreate all the Doc Sets from scratch. Worked for me.
Turns out I caused the issue myself. I renamed a file in siteUrl/_cts/DocSetName/. The proper would have been to delete the default content from the document set settings page, then upload a file with the corrected name.
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