I've had the same problem. It eventually resolved itself after
randomly occurring for weeks. I've made some code changes (which
seemed unrelated) so I cannot say for sure if Google made some changes
or I did by chance. Do you use transactions in your code? I seem to
remember that I had a massive transaction near the end of the handler
which I subsequently split into smaller writes and tasks.

It's fairly easy to debug. Just add logging to the last line of the
handler (or whatever the equivalent is in Java). In my case the
logging occured, but the backend didn't stop, even though there was
obviously no code left. My theory was that the backend didn't get the /
_ah/stop/ signal for whatever reason.

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