For large upgrades, where the system will be unavailable for hours, the process should be:
Disable auto-sync before an upgrade
Run a full silo sync after an upgrade
Enable auto-sync after the sync.
For smaller upgrades, like this one, where the system was only down for 30 minutes, it should be okay to skip the full sync, so the process would be:
Disable auto-sync before an upgrade
Enable auto-sync after an upgrade.
In general, it is really important to validate that no dependencies in the custom code (which use DFS and Digizuite) require Digizuite to be online. Ensuring resilience in the software architecture is key by allowing the site stay online even though access to certain parts offline.