The way that fastmap works is that in the local context of the transaction, it is doing a delete and recreate of the service.
The delete is automatically handed by the reverse diff that is stored with the service. I believe the service has created the ATOS routing instance, so that the routing instance and everything underneath is removed by the reverse diff.
Then your create code runs to recreate the service so at this point it is correct that it does not see the ATOS routing instance.
That also explains why the static routes added under the routing instance manually are disappearing, the reverse diff just removes the whole routing instance but you code only recreates the static routes it knows about.
For a quick test you could try to create an empty routing instance first, then create the service, then add some static routes then do a service redeploy. During creation the only thing that was created are the static routes, because the routing instance was already created by hand, so the reverse diff only removes those routes, and not the manually created routes.
I'm not sure how to fix your service, because I'm not sure of the exact effect you want to achieve, but one proposal might be to create the the routing ionstance in the pre-modification callback, outside of the scope of fastmap, that would behave very much like the test where you manually create it beforehand. However do note that if you change things that way, when you remove the service the routing instance is not removed.
