EmberJS Reset Warning: Library is already registered with Ember

Some background...

We have an ASP.NET app we're slowly converting over to EmberJS. We have a single Ember application we instantiate for certain portions of the site. As we migration pages they get routes in the Ember app. The goal is to have everything in Ember over time. In the interim, the user can click on links that take them back to ASP.NET portions.

Our issue is with resetting the state of the Ember app if the user either clicks back to go back into Ember or clicks on a new link that takes them back into the Ember portion.

We've tried calling .reset on the application, but doing so gives us an error saying the following. Our application is called ConsoleCli and not the standard App.

Library "ConsoleCli" is already registered with Ember

Moreover, we get the following error saying one of our modules has already been registered.

Cannot re-register: `location:history-js`, as it has already been resolved.

I tried wrapping my registration of the history module with a check, but that creates a whole other slew of errors

if(!application.__container__.lookup('location:history-js')){
    application.register('location:history-js', HistoryJsLocation, { singleton: true });
}

I read http://ift.tt/1EvtEln and I think it means reset() is supposed to clear all registries once this has all been merged into the main branches.

Shouldn't called App.reset() right in the middle of using an EmberJS application just reset it with no issue?

Excuse my lack of understanding, we're just learning all of this as we go.

We're running the following versions

Ember 1.11.0-beta.2
Ember Data 1.0.0-beta.15
jQuery 2.0.3

TIA!