My understanding from my vendor (GoDaddy) is that any certificate which expires after 2017 must be issued with SHA-2 algorithm. Therefore if you renew for three years they have to use SHA-2.
Domino does not (yet) support SHA-2 and it is unclear if it ever will. If you are running under the Windows OS the IHS (IBM HTTP Server) is an option for you. But domino under other OSes (we are using Linux) have no such option.
GoDaddy support promptly credited my account and reissued the order for a two year renewal so I could get the certificate with an SHA-1 algorithm. The only thing I lost in the process was one month on the certificate.
At the recent MWLUG conference IBM Product Managers heard from several attendees that something needed to be done and that sooner was critical because it was already costing users effort and money. Hopefully there will be a fix.