I'm currently running OwnCloud server 8.2.8 (latest 8.2), which I upgraded multiple times starting from 8.1.x using the updater app. I'd like to use the same app to upgrade to 9.1.x, but I don't see this option. I was able to upgrade between 8.1 and 8.2 major releases, but not to 9.0. Is this working as intended? Do I need to download the source and manually replace it to get a newer version?
Do a manual upgrade, it is more reliable. You can't upgrade to 9.1 directly, you must go to 9.0 first. If you use LDAP, make sure all calendars and contacts have been properly converted for all users before going to OC 9.1.