I can only think of that you deleted the meta package on some servers,
hence there are only new kernel packages available, but no meta package
to pull them in.

** Changed in: apt (Ubuntu)
       Status: New => Incomplete

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  apt-get update doesn't get new packages

Status in apt package in Ubuntu:

Bug description:
  apt-get update and upgrade do not upgrade the system
  --Steps to Reproduce---
   apt-get update and apt-get upgrade.  It shows nothing to upgrade. But the 
kernel level is in an old version. 
  New kernel packages are not shown in apt-cache. Somehow, the new packages are 
not being got from repo server when do apt-get update.

  Executed on 16.04.3

  Btw, not all the Ubuntu servers have that issues. I crossed check the
  sources.list among the servers, there is no difference. So don't know
  what caused some of them cannot get any update from ubuntu repo.
  However, I can install individual packages via apt-get install

  There is not any error during the apt-get update && apt-get upgrade.
  It showed nothing to upgrade.

  Hit:1 http://ports.ubuntu.com/ubuntu-ports xenial InRelease
  Hit:2 http://ports.ubuntu.com/ubuntu-ports xenial-updates InRelease
  Hit:3 http://ports.ubuntu.com/ubuntu-ports xenial-backports InRelease
  Hit:4 http://ports.ubuntu.com/ubuntu-ports xenial-security InRelease
  Reading package lists... Done
  Reading package lists... Done
  Building dependency tree
  Reading state information... Done
  Calculating upgrade... Done
  0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

  The servers were able to manually upgrade for a long time. But all the
  sudden, they are not upgradable. It looks it can not retrieve new
  kernel level packages during the apt-get update. The highest kernel
  level can be installed is 4.4.0-97.. not more higher..

  HWS: I mirrored this problem description, to be able to get support
  for getting this fixed. Even it seems to be an environment problem.
  But direct Q&A will probably help....

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