One of the great options provided by Availability Groups, in SQL Server 2012 Enterprise Edition and newer, is the ability to perform rolling upgrades to new Service Packs or Cumulative Updates.

The basic idea is that you apply the update to one of the AG secondary servers and then perform a failover of SQL to that server which then does the necessary things on the user databases to bring them up to the level of the update. The big advantage to this is that it minimizes the outage required to get the SP/CU applied, so that you are down for a few seconds instead of 40 minutes.

This is works really well for your regular user databases, however there is a problem when applying a CU or SP to a secondary server where a Integration Services (typically called SSISDB) is a member of an Availability Group. If you attempt to apply the CU/SP then it can fail and the SSISDB be left in an offline state. 

In order to apply the CU/SP you would first have to remove SSISDB from the Availability Group and recover it on each server you want to patch. Once you have completed patching all the servers you can add SSISDB back to the AG. But for that period of time you will be at risk, so get through and patch a couple of the machines and get the AG working for those as soon as possible.

Interestingly this does not apply for all CU/SP releases. Some do not make changes to SSISDB and this isn’t required. You can only find this out by patching, so be sure to get it going in your test environments first.