@Jeff
To help better understand your issue better, please find the following:
Has there been any changes in the QuickBooks file (change in the location of the file)?
Has your 'Change-Only' sync been successful?
I would also check your conflicts. Under QuickBooks > Resolve Conflicts, are there conflicts and when did they occur?
Conflicts should be resolved for the sync process to be successful. In our current version, under Resolve Conflicts, there is a button called Show advanced options... Selecting this button will reveal a section with a button to "Delete All 'Delete from Desktop'".
The function of this button is to clear all records that have been marked as 'Delete from Desktop'. This conflict most often occurs when you archive QuickBooks data, and Method finds that it now has data that no longer exists in QuickBooks. Be careful, clicking Delete All 'Delete from Desktop' is permanent. Note: this can take a long time, about 1 minute per 1000 records.
Please let me know if I can be of further assistance.