Yes, it seems to have something with pipelining, so I disabled it with
the following configuration:

    Acquire {
       http::Pipeline-Depth "0";
   };

I have some machines updating with this setting for 2 days without errors now. 
The performance impact seems insignificant (I have low RTT connections).
I also had the error occur on official mirrors, local mirrors with apache, and 
local mirrors with lighty before this.

I hope this helps fixing the issue.

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https://bugs.launchpad.net/bugs/1801338

Title:
  apt fails to properly handle server-side connection closure

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