Hello ​@John Robert 

I have done some digging my self and it seems that the API’s according to the documentation have no mention of the certificate. This is true for editing an existing app or creating a new app. 

I’m sure this is in the pipe line to get fixed up but to get a better timeline and make sure Dev know this is a thing customers want i recommend raising a support ticket. In this support ticket mention the following while requesting for either  CMR number that already exists or creating a new one. 

Steps wanting to follow vire API: 
https://docs.metallic.io/metallic/use_custom_configuration_to_add_azure_apps_for_sharepoint_online.html
 

Or: 
https://docs.metallic.io/metallic/generate_azure_certificate_for_existing_azure_apps_in_sharepoint_online.html
 

I know this was not the answer you are looking for but i hope it helps!

Kind regards
Albert Williams