We have developed our own implementation of zero downtime restage. We are using java client api version 3.14.0 RELEASE. As part of that

(1) we retrieve the ApplicationManifest from the old application <old name> that we need to restage using Applications.getApplicationManifest
(2) Create a new app <app name> using the Applications.pushManifest using the manifest from previous step. 
(3) Copy the bits using Applications.copySource from <old name> to <new name>

However, if I am using custom domains - then the step (2) creates a dummy app which has incorrect routes. Instead of the route being <custom domain>/<path>, the route cassociated with the new app is <app name>.<custom domain>/<path>. The <app name> is incorrectly added to the route as hostname whereas it should have been empty