The hash symlinks are supposed to be managed automatically by openssl.  If you 
have a symlink like
  /etc/ssl/certs/f066f19f.0 -> /usr/share/debathena-ssl-certificates/mitCA.pem
then it will get removed by c_rehash (which is run by update-ca-certificates).

However, if you instead make a symlink
  /etc/ssl/certs/mitCA.pem -> /usr/share/debathena-ssl-certificates/mitCA.pem
then c_rehash will add the symlink
  /etc/ssl/certs/f066f19f.0 -> mitCA.pem
and this will all be preserved over ca-certificates upgrades, etc.

Alternatively, if you put a CA certificate in /usr/share/ca-certificates
with the .crt extension, then run dpkg-reconfigure ca-certificates and
tell it that you trust the new CA, it will be linked to /etc/ssl/certs
appropriately and added to /etc/ssl/certs/ca-certificates.crt.

So this is not a bug, although there could perhaps be better
documentation.

-- 
ca-certificates removes all users certificates in /etc/ssl/certs
https://bugs.launchpad.net/bugs/114495
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