Hi Trent,
Unfortunately there is no easy way to delete Estimates in bulk in Method, however you do have some alternatives.
The easiest solution, would be to change the time period you are syncing for your Estimates from QBO to Method. The default setting for this is 31 days, for all transactions, however you have the option to change this value either for all your transactions at once, or individually. I realize you might have already found this option, if you are already showing over a years worth of Estimates in Method.
Either way, this setting is located in Method, go to QuickBooks->Synchronize, then scroll down the screen until you see the label, "Transaction history", the dropdown option directly below is a global setting, for ALL your transactions. However, if you click on the "Show options per transaction Type (click here)" link, you will see an option to individually choose transaction history's from there. If you want to keep the rest of your transaction history as is, then I would advise you to choose the individual option for Estimates, and lower that value to less than a year, or whatever desired range you want.
Technically you do have another option, however I am not sure this would help you out much. We could do a Reset on your Method account, this way your whole Method account would get wiped, and you could then resync with your QuickBooks account. Just keep in mind, you would run into the same issue if you extend the transaction history of your estimates right away.
Please let me know if this helps,
Ben