As per my discussion with Chris Waters today, would be ideal to have a warning message for the following scenario:
Have a warning message that only when time has already been logged (either at feature or requirement level) and you are then changing the core calculation of capacity burn down from one or the other that you get a warning message to advise that time logged in the other method will be ignored. This will then leave the responsibility to the user to either continue with the switching of time entry from one to the other with the knowledge that time already logged will be ignored from the capacity burn down.
From our business perspective we are going to instruct user to NOT proceed with the switching of time if it has already been logged as this has a direct impact to the synching between Aha burn down and our invoicing system which we have Aha integrated with.