Assuming that you want to keep the highest version (3.1) the 'path of least resistance' is to backup the 3.0 courses and restore them to the 3.1. Backups can be set for full .. keeping all data in a course ... or you can choose what to backup. The one item that might hickup is when an admin level user in the 3.1 also exist in the 3.0 backup of a course. Also, if there are any addons in the 3.0 that was being used in the 3.0, make sure you have the same plugins installed in the 3.1. You might need to research those as some plugins/addons don't make the trips to higher versions of Moodle.
'spirit of of sharing', Ken