Per the Prize Parameters, the positions of specimens, unit trays, labels, and other elements in the Entrant's drawer must be those outlined in the specifications for the surrogate drawer. The only allowed human intervention is the placement of the entire specimen drawer in the imaging station developed by the Entrant. Human manipulation of the positions of specimens, labels, unit trays, or any other elements within the drawer is not permitted once the specimen drawer has been placed in the imaging station. Further, if a pin is removed from its original location by mechanical means, it must be returned to the precise original location and position. Lastly, outlined in the "Beyond_the_Box_Complete Rules_Final" document, entries will be partly judges on how well labels are returned to their original positions.
Based on your example below, you would be in violation of the rules as the only allowed human intervention is the placement of the entire specimen drawer in the imaging station. Human intervention may not be used to return specimens, labels, pins, or other elements to their positions. It is expected that this would be included as part of the entire digitization process.