Is there any guidance/documentation available on the best approach to take when upgrading an distributed installation of FME server based on the Azure marketplace images?
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There's the general FME Server documentation about upgrading that you can use as a starting point: https://docs.safe.com/fme/html/FME_Server_Documentation/AdminGuide/Upgrading.htm
On top of that we always recommend to document your installation process so you can use that as a guide for the next one.