Nathan-
There was nothing you could do to fix this. The issue was that Intuit changed the way notes were handled and didn't inform any third-party companies so it broke the sync process. We have updated Method to work with the changes made by Intuit.
-Michael
Michael Melo
Product Manager
Method Integration Inc.
Website: http://www.method.me
LinkedIn: http://www.linkedin.com/in/MichaelMelo