Hi Jacob,
When Method is configured properly it shouldn't synchronize with a non-corresponding QB file. Referring to post: http://methodintegration.com/cs/forums/p/770/2624.aspx#2624 should help to resolve this issue.
Another possible reason this issue would arise is if within Method you go to Customize > Synchronize and click "Reset" for QuickBooks file to sync with. This tells Method that there is a different QuickBooks file to sync with. This button should only be clicked if you perhaps changed the name of the QuickBooks file but it must be the same QuickBooks file that was originally used.