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I'm going to assume everyone experiencing this issue is using M/S. Upgrading to HRD will solve your issue.This is the reason I abandoned AE and part of why adopting a platform that isn't standardized is incredibly dangerous. The problem is technical debt constantly accrues even when you aren't making changes.
Even though the API was unchanged, HRD differs subtly enough that breakage can occur on any non-trivial project. Edge cases (how indices behave within transactions comes to mind, but there are plenty more examples) will see new semantics compared to M/S, and so this "upgrade" involves not only thorough testing and auditing, but likely also code changes and potentially significant engineering hours.
http://goo.gl/HVuaC: These techniques are not needed with the (now deprecated) Master/Slave Datastore, which always returns strongly consistent results for all queries.
This means a project written and signed off circa 2011 requires mandatory engineering costs just to continue running in a functioning and supported fashion. An AE app will never quite resemble that ancient perl5 behemoth running uninterrupted since 1997, as the underlying implementation and recommended APIs are constantly modified and replaced (Datastore, NDB, Python major version).
"A strong test suite will save your soul!" I hear you say, tests that a small project might have survived without if targeting any other platform, and testing on AppEngine is also yet another moving target (for example, testing nested subrequests was all but impossible using the SDK until relatively recently).
The promise was a carefree life for a project willing to code against their proprietary APIs; the reality is a constantly moving target, "not quite free" autoscaling and the threat that while you're asleep an unannounced change will take down your app (I could name a few, but as many will attest this has happened regularly since launch).