I just noticed that fail2ban has been set up by virtualmin (or webmin) with its own jail.local file. I have some filters of my own, based on earlier hacking attempts, to keep people (rather bots) away which show a certain access pattern. Can I add these filters to the jail.local file, or should I add (and link) another jail-file? The question arises because it is likely that Webmin or Virtualmin might overwrite jail.local at any time, losing the settings I added.
Webmin/Virtualmin does not overwrite config files. We parse and edit config files. So, if you configure your services via CLI or other tools, Webmin/Virtualmin will generally not have a problem with it (assuming valid and parsable configuration files after your edits).