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I have removed a (root) certicate, and re-run update-ca-certificates:

$ sudo rm /usr/local/share/ca-certificates/mine.root-ca.crt
ls -l /usr/local/share/ca-certificates/
total 4
-rw-r--r-- 1 root root 1838 Feb 16  2017 something-else.crt
$ sudo update-ca-certificates
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.

But:

$ ls -l /etc/ssl/certs/mine.root-ca.pem
lrwxrwxrwx 1 root root 53 Jun  4 07:22 /etc/ssl/certs/mine.root-ca.pem -> /usr/local/share/ca-certificates/mine.root-ca.crt

But that file (/usr/local/share/ca-certificates/mine.root-ca.crt) does not exist anymore.

Actually, the 0 added, 0 removed; done. is suspicious: it should say 1 removed.

Certificate validation does not work anymore for the domain in question (as expected), but these two facts annoy me:

  • the lingering link
  • the fact that update-ca-certificates does not seem to do anything

I am in:

$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 16.04.4 LTS
Release:        16.04
Codename:       xenial
1

According to the man pages for update-ca-certificates, add the -f switch to remove symlinks in /etc/ssl/certs

-f, --fresh
          Fresh updates.  Remove symlinks in /etc/ssl/certs directory.

This will create a new ca-certificate.crt file without your root CA certificate and remove the symlink.

sudo update-ca-certificates -f

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