AD Federation Services failed after renewing SSL Certificate: How to Resolve

Recently I had to renew the SSL certificate for my AFDS Server and ADFS Proxy, both of which expired in Aug. We installed the ADFS and ADFS Proxy servers in the blog post Road to Lync Hybrid as we configured Lync 2013 for a Hybrid configuration with Office365. That Lync environment has since been upgraded to Skype for Business 2015. Generating a new CSR and obtaining a new cert was the easy part, however problems started appear shortly after for users who were dirsync'ed from AD to O365. They were unable to sign in to the Office365 portal and could not login to Exchange Online from either internal network or external network. Users hosted on Skype4B on-premise servers could still login to Skype5, but only from internal network. Users not dirsync'ed from AD continued to work as normal.

I started checking on the ADFS Proxy server to ensure that the newly installed certificate was indeed correct and it was. But the Event Log was showing error "Event 364 Encountered error during deration passive request":

A quick search on the internet on this Event ID turned up several possibilities including time skew between the ADFS and ADFS Proxy server, services not running on the ADFS server and certificate mismatch. None of these was happening so I decided to re-run the ADFS Proxy Configuration Wizard, which ran successfully except for a warning that the existing website was detected and not re-installed:

Clickong on the above link led to nowhere so further searching on the web provided a way to actually force the ADFS Proxy Configuration Wizard to re-deploy the website. This is done by running the following in a command prompt after which the website will be redeployed when running the wizard:
C:\WindowsSystem32inetsrvappcmd delete app “Default Web Site/adfs/ls

But the problem was still not resolved, but this time a different error was showing on the Event Viewer. An Event ID 248: The federation server proxy was not able to retrieve the list of endpoints from the Federation Service":

Results from the search query of the event error suggested this could be due to changing the "federation service identifier" from the default http://adfshostname.yourdomainname.com/adfs/services/trust from http to https. This was not the case however, in my server and another possibility that came back was that the ADFS 2.0 Token-decrypting and Token-signing certificates had to be renewed. So I opened up powershell and ran the following cmdlets as advised:

Add-PSSnapin Microsoft.Adfs.PowerShell
Update-ADFSCertificate -Urgent

With that, there were no new errors being shown in the event viewer, but users could still not sign-in into the Office365 portal using their AD credentials, but this time a different message was being shown on the IE page. This time, although we get directed to the ADFS web login page but entering the credentials shows a message:  "An error has occurred, invalid SAML token." With this error message, I found this support KB https://support.microsoft.com/en-us/kb/3015526 which indicates a known issue with Azure AD. As stated in the article, to resolve this run the following command in PowerShell on the AD FS server:

Update-MsolFederatedDomain -DomainName [verified domain]

Where the [verified domain] is the shared SIP domain for the hybrid setup, which in my case is "ucprimer.com":

With that, all ADFS services started working again and users dirsync'ed from AD were able to sign-in into the Office365 portal using their AD credentials as well as login to Exchange Online and Skype for Business Online and OnPrem. Hopefully this blog post will help anyone facing similar issues with ADFS. I'm certain this post will come in handy in a year's time when I have to renew my ADFS SSL certificates again.