While self-update
worked for you, that command is used for updating nitro itself. This may have the side-effect of updating your container, but if nitro is already up-to-date it may not do anything. However, the documentation lists multiple commands that are used to update your containers and environment:
nitro update
updates containers to their latest version.
nitro init
initializes or reconfigures the environment, presumably also refreshing the certificates.
nitro trust
installs the root certificates required for browsers to trust self-provisioned certificates (might be necessary after an update).
Beyond that, docker containers are there specifically to be ephemeral, so destroying and recreating them should never be a problem.