If you create a new LongStringProperty, it will, as you correctly guess, get a new guid id. So for the system, they will appear as two different properties.
I would suggest the following procedure:
Create the new longstring property
To copy the existing data in the shortstring column, you can create a workflow, and set the new longstring property value from the shortstringproperty value.
Another alternative (and quicker) is to use SQL directly on the database. Find the tablename of the relevant class, and use one of the examples from here: