It's important to separate the notions of device tokens and authentication tokens (also sometimes called "provider tokens" in the APNs docs).
Device tokens are analogous to a phone number and are used to address a notification to a specific app running on a specific device. Device tokens are unique to a specific app/device/environment (production or sandbox) combination, but don't change as a function of your authentication strategy.
Authentication tokens are completely distinct from device tokens, and are created by the sender using a private key issued by Apple. Authentication tokens have a short lifetime (an hour), and can be used to authenticate requests to send notifications to multiple devices. You can think of authentication tokens as short-lived API keys for sending notifications to all of the "topics" that you own.
That said, changing from certificate-based authentication to token-based authentication will have no effect on your existing device tokens. Everything will continue to work just fine.