Maciej, If you see an issue, re-run with debug::acquire::http so you can
see if the correct files (by-hash) are fetched. It works for me

# apt update -o debug::acquire::http=1
0% [Working]GET /ubuntu/dists/xenial-updates/InRelease HTTP/1.1
Host: us-east-1.ec2.archive.ubuntu.com
Cache-Control: max-age=0
Accept: text/*
User-Agent: Debian APT-HTTP/1.3 (1.2.32)


Answer for: 
http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/xenial-updates/InRelease
HTTP/1.1 200 OK
Date: Thu, 12 Dec 2019 13:48:46 GMT
Server: Apache/2.4.18 (Ubuntu)
Last-Modified: Thu, 12 Dec 2019 13:15:00 GMT
ETag: "1aa8c-59981884afd00"
Accept-Ranges: bytes
Content-Length: 109196
Cache-Control: max-age=0, proxy-revalidate
Expires: Thu, 12 Dec 2019 13:48:46 GMT

Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates InRelease 
[109 kB]
29% [Working]GET 
/ubuntu/dists/xenial-updates/main/source/by-hash/SHA256/4c90cfd51700c92be5e841e81f22c09cd620f2ecd4eb5712f0ba1df74f3f253a
 HTTP/1.1
Host: us-east-1.ec2.archive.ubuntu.com
Cache-Control: max-age=0
Accept: text/*
User-Agent: Debian APT-HTTP/1.3 (1.2.32)


Answer for: 
http://us-east-1.ec2.archive.ubuntu.com/ubuntu/dists/xenial-updates/main/source/by-hash/SHA256/4c90cfd51700c92be5e841e81f22c09cd620f2ecd4eb5712f0ba1df74f3f253a
HTTP/1.1 200 OK
Date: Thu, 12 Dec 2019 13:48:47 GMT
Server: Apache/2.4.18 (Ubuntu)
Last-Modified: Thu, 12 Dec 2019 10:36:41 GMT
ETag: "54038-5997f521bc040"
Accept-Ranges: bytes
Content-Length: 344120

Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main 
Sources [344 kB]
Fetched 453 kB in 1s (350 kB/s)  
Reading package lists... Done
Building dependency tree       
Reading state information... Done
All packages are up to date.

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https://bugs.launchpad.net/bugs/972077

Title:
  apt repository disk format has race conditions

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