During the Toronto Insider event, there was a feedback about Admins being able to set the defaults for all users in the company. When asked if the new defaults should be applied to existing reports/ projects, the suggestion was to leave those as-is.
I would suggest to add a prompt instead to ask the user if they would like to apply the new defaults retroactively, leaving this action to the Admin(s) and also giving them an option to roll back where necessary.
