Kenneth Busby
I had the same problem and it finally resolved by copying the folder (that contain the files you want to open through hyperlink) to the C://intepub/wwwroot directory.
For example my folder name was SMS_HPL (it contained all scanned maps as pdf files)
My server name is main-gis-01.abc.com
the file I want to access though html popup is Misal_Colony_DistributionMap.pdf
so, the path is https://main-gis-01.abc.com/SMS_HPL/Misal_Colony_DistributionMap.pdf
Make sure you configured the popup window in your web map.
Hope it will work.
Nadia