As soon as you start to keep your issue's content in sync by using Backbone Issue Sync, you have two issues with the same content: one issue is in project A and the other issue in project B. After a while you might run into the situation that you or your partner thinks an issue is not needed anymore and deletes it. This is not a problem as long as the other side does not update its copy of the issue.
Backbone does not synchronize the deletion of an issue.
This means, even though one side in your synchronization deletes an issue on their side, the issue still exists on the other side. You need to manually delete it from the other side.
For example: When you delete an issue in project A, then the synchronized issue in project B won't be deleted by Backbone. However, if you update the issue in project B and you configured Backbone to synchronize changes back from project B to project A, then an Issue Does Not Exist error will appear in the troubleshooting section of your synchronization configuration. This error will give you the opportunity to synchronize the remaining issue with a new issue or simply ignore future changes.