Thank you for explaining that.

It is sad and ironic that synaptic was deliberately changed (according
to comment#1 at
https://bugs.launchpad.net/ubuntu/+source/synaptic/+bug/42178#bug-
branches-container) to use /var/lib/synaptic/preferences instead of the
global preferences file /etc/apt/preferences

I think synaptic is actually more confusing because of that change! I
agree with what you wrote on the bug report. I too would like to see the
2004 change reverted, so that synaptic uses the global preferences file
in future.

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https://bugs.launchpad.net/bugs/1166568

Title:
  [update-manager-core] do-release-upgrade removing pinned / locked
  version packages

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