Uninstalling Structure
You can uninstall Structure from the Add-on Manager the same way you uninstall other add-ons. You can also manually remove the Structure JAR from the plugins/installed-plugins directory when Jira is not running.
When you uninstall the Structure add-on, Structure data is not removed. It remains in the Jira database.
Reinstalling Structure
It is perfectly safe to uninstall Structure, then install it again. (This happens, for example, when you upgrade to a newer version.)
All Structure data will be there unless you manually remove it.