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What you are describing is different from what I am seeing. You can follow the path I am taking in the workflow I appended above to see how the tasks are related. In my test I am doing this set of tasks and seeing which tasks are still reserved afterwards. The ones I am marking bold should not still be there:

1. Start Workflow
   1. Submit for Approval
   2. Modify Rule
2. Submit for Approval
   1. Modify Rule
   2. Approve Rule
   3. Reject Rule
3. Reject Rule
   1. Modify Rule
   2. Submit Rule
4. Submit for Approval
   1. Modify Rule
   2. Approve Rule - orphan
   3. Reject Rule
   4. Approve Rule
5. Modify Rule
   1. Approve Rule - orphan
   2. Reject Rule - orphan
   3. Approve Rule - orphan
   4. Submit for Approval
   5. Modify Rule
6. Submit for Approval
   1. Approve Rule - orphan
   2. Reject Rule - orphan
   3. Approve Rule - orphan
      
   4. Modify Rule
   5. Approve Rule
   6. Reject Rule
      
7. Approve Rule
   1. Reject Rule - orphan
   2. Approve Rule - orphan
   3. Modify Rule - orphan
   4. Approve Rule - orphan
   5. Reject Rule - orphan

When I check to see if the process instance is complete, it is not. Even the tasks in the subprocess are not being made not active, when I set the end node in the subprocess to terminate. You had mentioned that all tasks need to be complete or otherwise not active, so I am guessing this is why the process instance is still active. What would be the best approach to make the orphaned tasks not active? Any help would be appreciated.