ADFS is not available for upgrade, You have to remove ADFS role on the server and add this role again then
Then Setup Adfs with this link
docs.microsoft.com/.../setup-deploy-on-premises-pu41
Once you done this the system gives you an error to your client id is not match on the adfs server cause of you create a new application group and the client id are different. You can change the setting on the lcs and re-deploy your envoirements.
Or you can change ADFS client ids
Microsoft Dynamics 365 for Operations On-premises - Native application
Microsoft Dynamics 365 for Operations On-premises - Financial Reporting - Native application
and change the relying part identification
Microsoft Dynamics 365 for Operations On-premises - Web application
Then re-start all servers and node.
I hope this ll help