Once you run "Update your tickets!", the tickets are installed directly in to your NAND (if you're using 0.2). You will need to use something like FBI to remove each ticket individually if you want to clean up what it's done.
Thousands of tickets!!! it's not possible remove one by one.
How about a simple solution:
Enter 'GodMode9', delete CTRNAND/dbs/ticket.db.
What do you think?