Hi there TomH,
How long roughly are we talking before the Estimate 'disappears' from Method? Are they still visible in QuickBooks? Its possible these Estimates have simply fallen outside of the Transaction History which Method Keeps for your Quickbooks Transactions.
By default - a 31 day Transaction History is maintained for your closed transactions - at which point it is archived on the Method Side (but untouched on the QuickBooks side!), and ignored by the sync process. We keep this transaction history short by default to make sure that the Sync is as speedy as possible, and not getting tied up in ancient transactions you dont need to see anymore.
That being said - If you would like to Increase the Transaction History - that is also possible! Take a look at This Help Centre article (Method:New), and follow the steps to set how far back you wish to sync your transactions.
If this doesnt fix your issue, let me know and I'll take a look at your account to see whats happening.
Thanks TomH
-Ben