There shouldn't be any issues with deploying the same code twice or more as it will result in different App Engine versions. It doesn't seem like there is an option to deploy multiple versions of the same services to App Engine though you can deploy different services in one gcloud command[1].
[1] https://cloud.google.com/appengine/docs/flexible/nodejs/testing-and-deploying-your-app#deploying_multiple_services -- You received this message because you are subscribed to the Google Groups "Google App Engine" group. To unsubscribe from this group and stop receiving emails from it, send an email to google-appengine+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/google-appengine/5276db3c-fc0d-46f4-a0c9-cdc84bc95dfd%40googlegroups.com.