Updating Always On Availability Group server connected to Windows SQL Cluster I'm working with a unique configuration.  Our organization prefers Windows Failover Clusters for our main database servers.  In this case my primary replica is a WFSC.  This is a reporting server where the data is extracted to each night.  We have a large database that we duplicate to another server we call shadow.  The shadow server supports the secondary replica.

I don't have a lot of experience adding updates/service packs to this configuration because of the business requirements to keep it running.  That said, I'm wondering if anyone has experience with updating WFSC &amp; Always On availability groups and can give me some pointers.  I'm concerned with how the AG will react to different configurations when we roll the WFSC from one node to the other.
It will not react any different, it is the same way as you upgrade a cluster server (if you did that before). To minimize the downtime of your server make sure to set it up a manual failover. Then start with patching your secondary node after you finish that, do database consistency check, on your secondary and then failover the primary node to your secondary server (the updated server) and do the same exact process on the then primary, now secondary node. Once you finish the upgrade make sure to check the health status of the availability group and if fix if any suspended or not synchronized database on from the list of your availability database.