Hello Jason,
I would strongly avoid condensing your QuickBooks file if it is connected to a Method account. It would have adverse affects on the Method database. You would run into very large problems including many conflicts.
The article you have read is not an official Method article from the Method Help Center. Data corruption or errors with the QuickBooks file can come up in the Resolve Conflicts list. This is out of Method's realm to help fix the data corruption errors in QuickBooks. Some companies do solve it by doing a Verify & Rebuild. If you do go the route of creating a brand new QuickBooks file, you will need to create a new Method account. Any data like leads that you want transfered over can be done via the import/export tolls in the Integration Tools screen.
I hope this helps,
Greg