I reached out to Eduardo about this last week. The problems he was having were temporary and went away on their own. The most likely cause of these issues was an upgrade that was applied to production around that time. Backend instances need to be shut down temporarily when these upgrades occur, which explains the "disappearing instances". The problem of failed deployment was likely a due to a temporary instability in one of the bigtables that App Engine uses. We monitor those types of problems and they are usually resolved after a brief period of failed (or slow) deployments.
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