I had been running the 2.5 beta for awhile now with no trouble other than a few bugs I fixed manually. Now that 2.5 is official, I took out testing from the repo and did a dist-upgrade. All is well, except since I modified those files I get the error below when I upgraded. Is there any way to force the re-configure of say Fail2Ban and overwrite my file?
Setting up yunohost (2.5.4) ...
Regenerating configuration, this might take a while...
Warning: The configuration file '/etc/nslcd.conf' has been manually modified and will not be updated
Warning: The configuration file '/etc/postfix/main.cf' has been manually modified and will not be updated
Warning: The configuration file '/etc/rmilter.conf' has been manually modified and will not be updated
Warning: The configuration file '/etc/fail2ban/jail.conf' has been manually modified and will not be updated
----EDIT----
Figured it out myself. Posting for anyone else.
sudo yunohost service regen-conf fail2ban -f