Please check to see if the Method Integration Engine is up and running and your Quickbooks file is open. If the sync engine is working, the customer you are deleting most likely has transactions associated with it. Also, if the QuickBooks file is currently in
Multi-User mode, QuickBooks will not allow customers to be deleted.
If customers have previous transactions, QuickBooks will not allow Method to delete them. If you check QuickBook -> Resolve Conflicts there may be a list of conflicts corresponding to the customers you tried to delete. From here you can click Delete From Method which will delete those customers from method but leave the customer and their transactions in QuickBooks.
To help you troubleshoot, expand the Customers and Contacts grid to show recordID and EntityRecordID by clicking the gear on the bottom right and updating. Try to match the EntityRecordID to any conflicts you may have.