Change the sort order of your register to Order Entered. This will put all the newly dumped transactions at the bottom.
Select the bottom-most transaction.
Scroll up until you reach the first newly dumped transaction. Shift-click it. This should select all the transactions you want to delete.
Press Ctrl-D to delete them all.
Restore your favorite sort order to the register.
Did you set the sort order to Order Entered? That "should" separate the new duplicates from your good transactions. You do have to accept the dups into the register.
I am advising you to literally sort by Order Entered in the register after accepting the dups. See: