Cezary, I was in the same position in August, with our Python apps on
M/S.
The DEE errors began to appear, then were more and more frequent and
finally had a high impact on our app availability.
Our warmup requests, that only load code, were randomly taking from a
few secs to more than 30sec and so triggering the DEE.

I could not figure out how it could be linked to the datastore, but
Google team only had one word to mouth: move to HRD.
No explanation at that time and made so sense for me but I decided to
trust them.

We migrated to HRD writing our own mapreduce and then all went fine
(except for the costs that went higher but hey, was the price for a
more reliable
solution).

But since something like mid-December, exactly the same symptoms
begin to appear again. Less frequent and not really impacting our
availability yet, but still there.
And no official acknowledgement of this issue so far...

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