have found the setting in Notes that will make those Calendar emails delete from the inbox instead of just removing them form the view. By default it just removes them from the view and hidden to the user so in realtiy it still exists in your mail file which is why it is still on your Blackberry. Please do the following steps:
Tools->Perferences->Calendar & To Do->AutoProcess.
If you check the bottom there is an option for Automatic Inbox Management. Change this to Prompt to Confirm Deletion.
Now when you delete a calendar entry the a box will pop up. Remember to Uncheck the "In the future, always remove Calendar and To Do entries..." and then click on Delete.
This fixed the issue