Endpoints: /_ah/api/ returns 404 after update - google-app-engine

Question

Problem fixed via Google Cloud support:
I removed the /_ah/spi/* handler from my endpoints yaml file, and the
- url: /.*
script: api.app
did not instantiate the endpoint.
It used to work before since the API was deployed for the previous version, but with the new version, there was nothing explicit to deploy the endopoints. So handlers need to be
handlers:
- url: /_ah/spi/.*
script: api.app
- url: /.*
script: api.app
Keeping the issue below for reference purposes
I've just deployed a new version of my application, and calls to http://app.appspot.com/_ah/api/app/version/method now return a 404. It worked perfectly before the update.
However, there's no trace at all in the logs, and no instance launched when I call/ping those URIs.
While if I call /_ah/whatever/app/version/method, I still have a 404, but it appears in my module logs, and it has the following message
{"state": "APPLICATION_ERROR", "error_message": "Not Found"}
The app is configured using modules, my app.yaml is defined with
application: appname
version: 2015-04-07
runtime: python27
api_version: 1
threadsafe: true
handlers:
- url: /_ah/spi/.*
script: api.api.app
- url: /.*
script: www.www.app
secure: always
libraries:
- name: pycrypto
version: latest
- name: endpoints
version: 1.0
- name: webapp2
version: latest
- name: jinja2
version: latest
And, in api/api.yaml
application: appname
module: default
version: 2015-04-07
runtime: python27
api_version: 1
threadsafe: true
inbound_services:
- warmup
handlers:
- url: /.*
script: api.app
libraries:
- name: pycrypto
version: latest
- name: endpoints
version: 1.0
- name: ssl
version: latest
I've updated the app to serve this new version in the admin console, and all other modules work perfectly.
Also, I can't see my API in the API explorer, https://appname.appspot.com/_ah/api/explorer returns an empty list (while I see it when running the dev server on localhost).
Update: I've just noticed, looking at #bossylobster reply in GAE cloud endpoints - Api not updating after deploy, that I do not have "Successfully updated API configuration" in my logs after the "Completed update of a new alternate version". However, I have "API deletion serving" at about the time everything started to be 404. Yet, I have no idea why there's this API deletion query in my logs. Any idea of what can be wrong?
That's an app in production and so the mobile version is down at the moment. I'm happy to send the app ID to a devrel in PM if that helps.