Microsoft 365 - Manage licensing tokens in hybrid environment (Azure(Intune) and Domain (SCCM))

On Monday of this week our systems stopped signing our users in directly to their Office365 applications (for most users) and now they have to sign in at every visit to their workstation or laptop device. We operated Shared Computer Activation and the relevant registry settings are in place but I cannot see where, if it is actually in place, the tokens are being saved.  I understand that they are generally stored in the appdata\local\microsoft\office\16.0\Licensing in a normal environment.  If they are not in that location I then assumed that they must be using roaming tokens but there is no Group Policy anywhere that indicates that this is the case. We operate a hybrid Azure (Intune) and Domain (SCCM) environment and I'm pulling my hair out trying to find how this should be managed and where the tokens should be stored to prevent the constant requests to sign in to access Apps. 

Any help would be amazing. 

Chris