Instead of requiring the user to add the new configs and strings or resetting the config, you can make the plugin do one of the following things:
Check for a config value like "config-version" that the plugin will check and, if the version is major, it will add the new defined config and variables.
Checking for each variable and config value and, if it's not in the file, add it. This method will make the plugin to need more time at startup.
Doing this would make the users who update but don't stop to see the news to know what is new, so then they will have the news in the file, so they can see that they are interested in that, so they see what's new and they don't get tired of "not getting anything new", when it's that they aren't reading updates.

Thanks.

Any of the config options that were added were not major and wouldn't break any old config files.
Automatically adding it is something I was planning to do but I am working to convert some YAML files to a single database file such as the first-join.yml and ip-limits before I do that.

Adding the config options for the user is a lot of lengthy code that is really unnecessary but it is something I have been looking into adding for v4.7. ItemJoin v4.7 is going to be more about utility and fixes rather than new features so expect that in the future :)

ItemJoin v4.8 has been officially released containing this feature for official usage.
You can grab it here; https://www.spigotmc.org/resources/itemjoin.12661/download?version=223327

It may not be used in v4.8 but it has been implemented for when this feature is needed to be utilized by the plugin.

Please read the changelog as the documentation has not been updated yet;
https://www.spigotmc.org/wiki/recent-changes