fail2ban should be re-scanning the jail target logfiles on (re)start and reinstating bans that should still be in force. This is not happening on my system: all bans are permanently dumped on restart.
I am using logrotate which I know is responsible for a lot of issues with fail2ban, but I can confirm that even non-rotated logs contain bannable strings (and these were correctly banned by fail2ban prior to restart) that are within the set bantime (let alone bantime+findtime) for the jails in question. I'll give full details if required.
I'm a little uncertain from reading the above upstream ticket whether the author's claim to have implemented this is correct, particularly as the ticket is still open. Perhaps the Gentoo package maintainer can clarify this and accordingly either address it here or upstream it. Thanks.