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We haven't made significant changes to the server lately.

More likely, OmniFocus had a stale .client file that it finally deleted. If you don't sync a device for a while, OmniFocus carries around a lot of history about everything that's happened since the last time that device synced. After a few weeks, OmniFocus gives up on that client ever syncing again, and cleans up that history.
Sometimes updating an OS or making other system changes can end up creating a new client file, so you might get into this state even if you keep all your devices synced daily.