Support and I were able to work this out. First, the HF files are only applied to the Client installation folder (C:\Program Files\SolarWinds\DameWare Mini Remote Control x64, in our case), and NOT the Agent folder (C:\Windows\dwrcs).
Then we built a new MSI using the Mini Remote Control Client Agent Builder and did not select any of the additional module or driver check boxes. This created an agent installer that passed our security vulnerability scans (the original reason for trying to use the HF files), but we couldn't connect to the remote agent using smart card. I then built a second new agent installer, but this time selecting the FIPS module and smart card drivers. This agent passed our vulnerability scans AND we were able to use smart cards to connect to remote agents.(It might be that the additional keyboard or mirror drivers are the files that pop the vulnerability scan, but I haven't had the time, or really the inclination to delve any deeper into the issue).