I guess someone else must have met this issue but I couldn't find anything out there.
We have installed ADFS on Windwos Server 2012 R2 to federate with O365. This works perfectly.
Then we added some "Additional Authentication Rules" (Set-AdfsRelyingPartyTrust –TargetRelyingParty $rp –AdditionalAuthenticationRules "...") to skip MFA for some applications. This also works well.
The issue is that after rebooting ADFS server these rules are not retrieved by Get-AdfsRelyingPartyTrust. They are still being executed since everything works as expected so they must be saved in the database but they cannot be managed with GUI or Powershell.
I get the known follwing error if I try to reset these rules with Set-AdfsRelyingPartyTrust:
"ADMIN0031: Configuring multiple policies of type 'StrongAuthentication' is not supported."
I know that MS advises to recreate the whole RPT to solve this error: https://social.technet.microsoft.com/Forums/en-US/bf0ebb20-05c2-4632-b213-7b9b61c604b9/setadfsrelyingpartytrust-syntax-error-assistance?forum=ADFS
But obviously you would run into the same issue when the server restarts after updates.
So my question is: Do your additional authentication rules (if you created any from Powershell) become invisible after reboot