If Quickbooks is assigning transaction numbers:  This means the numbers are being assigned by Quickbooks through their rules. To fix the sequence, you’ll have to ensure that it is fixed in Quickbooks. 

If Method is assigning transaction numbers: Method assigns transaction numbers by taking the highest transaction number and +1 it. For example, if you create an estimate with reference number 10, and then create an estimate and manually enter 500 as a reference number, the next estimate you create will have an auto generated reference number of 501. This takes into consideration deleted transactions, so even if you delete the estimate with reference 500 and 501, the next estimate will have an auto generated of 502. 

To fix the sequence, all transactions with high numbers will have to be re-numbered back down to sequence —including any deleted ones. If after re-numbering them the sequence is still high, there are likely deleted transactions with high reference numbers. Please contact Method Support for assistance.