Hi Vaughan1. Thanks for reaching out to the Community. QuickBooks Online is an easy-to-use program which makes it simple for you to navigate and get your work done faster. When it comes to deleting your transactions, using a third-party app is the best way to go especially if you'd like to batch delete the transactions. These third-party apps can be found on our app store using this link here.
The Transaction Deleter app (SaasAnt) you're using only deletes 1000 transactions at a time. This maybe the reason why some transactions are getting deleted while others aren't. Check out this article here which shows you how to use the Transaction Deleter app. I also recommend taking a look at other apps on our app store or you can manually delete the transactions from QuickBooks using the steps in this article here. Let me know how you make out. I'll be here.