A new version of ArcGIS Server Cloud Builder for Microsoft Azure is available with each ArcGIS release. An image that contains the latest version of ArcGIS software is also available at each release. The image and ArcGIS Server Cloud Builder for Microsoft Azure versions you use must match. For example, to deploy a web GIS using 10.3.1 images, you must use the 10.3.1 version of ArcGIS Server Cloud Builder for Microsoft Azure. Similarly, to deploy from 10.4.1 images, you must use the 10.4.1 version of ArcGIS Server Cloud Builder for Microsoft Azure. You can have different versions of ArcGIS Server Cloud Builder for Microsoft Azure on the same machine, allowing you to manage version-specific deployments.
You can upgrade ArcGIS software on existing deployments just as you do on-premises installations; however, once you've upgraded the software, do not use ArcGIS Server Cloud Builder for Microsoft Azure for postdeployment operations including registering databases with ArcGIS Server, installing CA-issued-certificates, and connecting to, or deleting these upgraded deployments.