After you send a settlement to QuickBooks, you can remove its sales invoice or journal entry from inside Taxomate.
If you matched the entry with the payment in your bank account, unmatch it first.
In QuickBooks, go to Transactions > Bank transactions.

Select Categorized.

Find the matched transactions and select Undo on the right, under Actions.

If Automatic sending is on, Taxomate can send the deleted entries again. Select Change next to "Automatic sending" at the top of Settlements (or Payouts) and turn it off first.
For one settlement or payout
Open the settlement.
Select More actions, then Delete entries from QuickBooks.
Confirm. (This item shows only after something was sent.)

For several settlements or payouts
On Settlements (or Payouts), select the rows.
In the bar at the bottom, select More actions.
Under Remove entries, select Delete accounting entries. (The label is the same for payouts.)
Confirm.

There is no delete button on the row. The row ⋯ menu has Open, Send…, Rebuild, and Archive.
Taxomate removes the sales invoice (or journal entry) from QuickBooks.