If you scanned or received a scan that was scanned incorrectly the annotations will be mixed up. Here is how you fix this,
-First you need to create a new order in your 3shape. Same name everything.
-Then you want to import in the scans again into that new order you have created doing lower first, then upper, then bite. If you cant bring in the bite don't worry. Sometimes it wont let you and it will be fine.
-To get to your scans you go to your C drive, 3shape, and they will be in there by last name.
-After you have done this, go ahead and start designing. Everything will now be in the order correctly.