Hopex V2 has a new feature of Building Process Diagrams automatically from a table view.
This feature is only available on web mode, this is why you get this message in web mode.
If you say that you want to lose your shape disposition, mega will calculate automatically the best shape position, and you'll be able to modify your process in a tabular view.
If you stay on the manual modifying mode, you will be able to modify the diagram as you want.
This is only available for diagram of processes in BPMN and on the properties of the diagram, you can choose is you want MEGA to automatically open the diagram in Manual, Table or ask the user each time.