I think I'm still hitting this issue 10 years later. On Ubuntu 18.04.1 I
was trying to add the 18.04.2 CD as a source to upgrade from. It would seem
to work and I could upgrade single packages, but if I would do an upgrade I
would get "File not found" for every package even though the paths being
referenced were correct. The "cdrom://" protocol being sort of obtuse
really made debugging it difficult. I randomly noticed in my output from
"apt-config dump": Acquire::cdrom::mount "/media/cdrom/"; even though
apt-cdrom automatically mounted the disk to "/media/apt". I decided to try
symlinking "/media/cdrom" to "/media/apt" and it started working properly!

So it appears that there's some disconnect in apt between "/media/apt" and
"/media/cdrom" and when to look at each, or "Acquire::cdrom::mount" is not
getting updated when apt-cdrom is being ran. A similar issue was posted
here -
https://www.linuxquestions.org/questions/debian-26/problems-with-apt-cdrom-add-command-866761/

Hope this helps.

-Jesse

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