Not sure if this is the right place to post, but here it goes.
I still have the same problem on the servers where virtualmin-nginx version is installed
root@server ~ # apt-get clean
root@server ~ # apt update
Hit:1 http://mirror.hetzner.de/ubuntu/packages bionic InRelease
Hit:2 http://mirror.hetzner.de/ubuntu/packages bionic-updates InRelease
Hit:3 http://mirror.hetzner.de/ubuntu/packages bionic-backports InRelease
Hit:4 http://mirror.hetzner.de/ubuntu/packages bionic-security InRelease
Hit:5 http://software.virtualmin.com/vm/6/gpl/apt virtualmin-universal InRelease
Hit:6 http://ppa.launchpad.net/ondrej/nginx/ubuntu bionic InRelease
Hit:7 http://ppa.launchpad.net/ondrej/php/ubuntu bionic InRelease
Hit:8 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:9 http://archive.ubuntu.com/ubuntu bionic InRelease
Get:10 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
Get:11 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
Fetched 163 kB in 2s (84.2 kB/s)
Reading package lists... Done
Building dependency tree
Reading state information... Done
3 packages can be upgraded. Run 'apt list --upgradable' to see them.
N: Skipping acquire of configured file 'main/binary-i386/Packages' as repository 'http://software.virtualmin.com/vm/6/gpl/apt virtualmin-universal InRelease' doesn't support architecture 'i386'
N: Skipping acquire of configured file 'main/binary-amd64/Packages' as repository 'http://software.virtualmin.com/vm/6/gpl/apt virtualmin-universal InRelease' doesn't support architecture 'amd64'
root@server ~ # apt list --upgradable
Listing... Done
webmin/virtualmin-universal 1.942 all [upgradable from: 1.941]
webmin-virtualmin-nginx/virtualmin-universal 2.6 all [upgradable from: 2.5]
webmin-virtualmin-sqlite/virtualmin-universal 1.6 all [upgradable from: 1.5]
root@server ~ # apt upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be upgraded:
webmin webmin-virtualmin-nginx webmin-virtualmin-sqlite
3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 17.2 MB of archives.
After this operation, 29.3 MB disk space will be freed.
Do you want to continue? [Y/n] y
Get:1 http://software.virtualmin.com/vm/6/gpl/apt virtualmin-universal/main all webmin all 1.942 [17.0 MB]
Get:2 http://software.virtualmin.com/vm/6/gpl/apt virtualmin-universal/main all webmin-virtualmin-nginx all 2.6 [108 kB]
Err:2 http://software.virtualmin.com/vm/6/gpl/apt virtualmin-universal/main all webmin-virtualmin-nginx all 2.6
File has unexpected size (108206 != 108220). Mirror sync in progress? [IP: 163.172.162.254 80]
Hashes of expected file:
- SHA512:eeb0101093aa6907ebac3baf527566a593b45cbe62d4300f2c7886613c1d629bbfb10a78f96f0ca0615506d23fa57026e6b0e10f45df37378c364d9e4e89150d
- SHA256:0eee763d023bc600671192a5f7dabc17eeb41b26ac90af9cf86d5e32994b90d9
- SHA1:3f692fdee0ba6f802329ec94eddd79240a46715c [weak]
- MD5Sum:de7542e8854d5ec6f3afb888022c7e56 [weak]
- Filesize:108220 [weak]
Get:3 http://software.virtualmin.com/vm/6/gpl/apt virtualmin-universal/main all webmin-virtualmin-sqlite all 1.6 [19.9 kB]
Fetched 17.1 MB in 1s (12.9 MB/s)
E: Failed to fetch http://software.virtualmin.com/vm/6/gpl/apt/pool/main/w/webmin-virtualmin-nginx/webmin-virtualmin-nginx_2.6_all.deb File has unexpected size (108206 != 108220). Mirror sync in progress? [IP: 163.172.162.254 80]
Hashes of expected file:
- SHA512:eeb0101093aa6907ebac3baf527566a593b45cbe62d4300f2c7886613c1d629bbfb10a78f96f0ca0615506d23fa57026e6b0e10f45df37378c364d9e4e89150d
- SHA256:0eee763d023bc600671192a5f7dabc17eeb41b26ac90af9cf86d5e32994b90d9
- SHA1:3f692fdee0ba6f802329ec94eddd79240a46715c [weak]
- MD5Sum:de7542e8854d5ec6f3afb888022c7e56 [weak]
- Filesize:108220 [weak]
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?