If you create a route in your theme's routes.json file, the route will not be deleted from the admin.

Simulation

Create a page on your themes under the routes.json file:

The page will be correctly created on the admin:

If you delete that route from the theme, the admin reference will still be there. But you will still be able to edit the routes on the admin.

Workaround

You can open a ticket to the support team asking to delete those routes.