Setup privacyIDEA with RADIUS and forget about Windows/NPS…
If your existing setup works with NPS, your RADIUS configuration page (on SoftEther) points to it…
Replace it!
If your NPS server is 10.10.10.10 and privacyIDEA server is 10.10.10.20 replace the first IP with the second on the SoftEther config page and you are done…
EDIT:
Are you sure the existing setup is using RADIUS with Windows AD?
What flavour of SoftEther do you use - open source or commercial?
Based on this discussion the free SoftEther does not support RADIUS