Besides some backward-breaking (though standard-compliant) behavioral fixes (see CHANGES), there are changes in version 3 which also unfortunately cause data stored under version 2 to break. We are not able to provide you with an automated upgrade path, so you will need to either stick with version 2 or migrate users' data yourself to the new SQL storage format (whose changes are considerable; CHANGES also lists these breaking database format changes).
We have attempted to anticipate future changes so that for another upgrade, even a major one, old data will hopefully continue to work. However, to be safe, if you are using npm, be sure to specify semver targets in your dependencies properly so as to avoid allowing for automated upgrades to the next major version in case another future upgrade may also need to introduce breaking changes to the data format, thereby breaking old data.