Notifications have stopped in some workflows and for some users after server upgrade

Have you checked the mail server logs? Could they being sent by the server but not received for some reason? Are the affected users' email addresses perhaps incorrect? 

I can confirm that the M-Files email logging clearly shows 2 of the 3 users emails being sent, with absolutely no reference to the 3rd user. Its like that user doesnt exist. I followed this process Collecting Logs for Email Server Connections and Emails sent by M-Files Server (site.com)

I can also confirm that when running a messagetracinglog on the exchange server it shows no trace of any email being sent from mfiles to the 3rd users mailbox, the other 2 users emails do appear. 

I can also confirm the affected users accounts are 100% correct as they are domain based and the information has been imported from AD. Normal emails work, their credentials to m-files work. Its just like the users have gone invisible in the system for anything automated. 

I can confirm that the M-Files email logging clearly shows 2 of the 3 users emails being sent, with absolutely no reference to the 3rd user. Its like that user doesnt exist. I followed this process Collecting Logs for Email Server Connections and Emails sent by M-Files Server (site.com)

I can also confirm that when running a messagetracinglog on the exchange server it shows no trace of any email being sent from mfiles to the 3rd users mailbox, the other 2 users emails do appear. 

I can also confirm the affected users accounts are 100% correct as they are domain based and the information has been imported from AD. Normal emails work, their credentials to m-files work. Its just like the users have gone invisible in the system for anything automated. 

When I say 3 users.. clearly the system has heaps of users I am just using the 3 users as an example in the above.

I'd raise this via your reseller. This doesn't sound right.