When a Version in JIRA is being renamed, the issues do not get updated (no entry in the changelog) - therefore Backbone does not sync the changed version.
Improvement
When a version is renamed, all issues which use this version in any version field, should be synced again.
Workaround
Perform a resync for the mapped version fields and all issues assigned to this version, a JQL might be 'fixVersion = "4.0.3"'.