Hi Ganbold,
Yes you could just deploy a new service with App Engine Flex configuration.
You will have to keep in mind the differences between App Engine Standard and Flexible[1] and how you can optimize your code[2] if needed, when doing the migration.
[1] https://cloud.google.com/appengine/docs/flexible/python/flexible-for-standard-users
[2] https://cloud.google.com/appengine/docs/flexible/python/migrating