The GAE services offer complete code isolation. So it should be possible to simply deploy a new version of the service, which can be written in a different language or even use a different GAE (standard/flex) environment. Personally I didn't go through a language change, but I did go through a split of a single-service app into a multi-service one, I see no reason for which the same principles wouldn't apply.
Maybe develop the new version as a separate app first, to be able to test it properly without risking an accidental impact on the old version and only after that bring the code as a new version in the old app. That'd be using the GAE project isolation. You can, in fact, test the entire version migration as a separate app if you so desire without even touching the existing app. I am using this technique - a separate app ID - to implement a staging environment for my app, completely isolated from my production app, see How to copy / clone entire Google App Engine Project
Make sure to not switch traffic to the new version at deployment time. This keeps the app working with the old version. Test first that the new version works as expected using Targeted routing. Then maybe use Splitting traffic across multiple versions to perform A/B testing with just a small percentage of the traffic going to the new version. Finally, when happy with the results, switch all traffic to the new version.
You need to pay special attention to the app-level configs (dispatch, cron, queue, datastore indexes), shared by all services/versions. They need to be functionally equivalent in the 2 versions. The service isolation doesn't apply to them, only project isolation can ensure no impact to the old version.
There should be no need to make any change to the app ID, custom domain mapping or SSL config. The above mentioned tests should confirm that.
A few potentially interesting posts related to re-working services/modules: