Ok, here are a few suggestions:
You can delete the Estimates from QuickBooks , and since Estimates don't post against Accounting, it should not be a big issue. Typically we always recommend for our users to not delete transactions though, as it is not best practices. If you choose to delete them, you can then go to those Salesforce.com Opportunities and remove all of their QuickBooks information, change their type to Invoice, and re-synch. Make sure to also go into the Opportunity Products and remove the QuickBooks information in the Opportunity Products.
Second suggestion is to void all of the Estimates ( can estimates be voided?) . Then go to Salesforce and do the same as in the first suggestion. Remove all the QuickBooks information from the Opportunity and Opportunity Products.
Last suggestion is to convert those Estimates in QuickBooks to Invoices. Then run DataSynch. DataSynch will then create a new batch of Opportunities in Salesforce.
Let me know if anything needs clarification , good luck!