Deleting or unlinking an account will remove all transactions associated with that account. Keep in mind: before you do any major deletions, you should download your GoDaddy Bookkeeping data into a CSV. To do so, please refer to the following article: http://help.bookkeeping.godaddy.com/entries/469838-How-do-I-get-my-data-out-of-GoDaddy-Bookkeeping
Here’s how to delete an account:
Starting from the Overview page, click on “Manage."
In your accounts page, find the desired account and click the “Delete” button.
Your account and any associated transactions will now be deleted. (Note: This will also delete any QFX files that have been associated with this account)