Migrating from SCCM 2012 App-V to Native App-V

Hi 
I've recently built a full App-V infrastructure ready to take over the delivery of App-V applications from SCCM to improve on a number of key areas. (We have about 50 App-V apps currently being delivered from SCCM 2012)
I found during testing that when I attempt to publish/stream to some test clients that are SCCM managed, publishing failed. I put this down to the
LocationProvider being configured to allow clients to access their applications from SCCM DPs. All sounds fair. When I configured
IgnoreLocationProvider =1, I was able to publish. 
I read Thamim's excellent blog here: http://virtualvibes.co.uk/configuration-manager-2012-sp1-and-app-v-5-0-integration-more-than-meets-the-eye/
Right at the bottom this statement became a concern: "Even though you may get the delivery working from App-V Full Infrastructure, sooner or later CM integration
will run the following commands to remove any publishing servers." 
So I guess my questions are as follows:
- What is the best strategy for this type of migration?
I guess I'll have to: A) populate my App-V infrastructure with all currently delivered SCCM App-V apps B) Publish them to appropriate AD groups C) Change the App-V GPO to
IgnoreLocationProvider so the clients receive the apps from App-V not SCCM and D) retire the SCCM App-V apps.  
- Is there any setting in SCCM that will kick back in and retake control of the App-V client to prevent publishing from App-V Native? 
Thanks 
David Murphy

haha thanks Rory
Motivation of going to App-V native is stateless VDI. 
We will continue to deliver App-V apps to traditional desktops via SCCM however we are getting burned in app delivery times and shortcut management for our stateless hosts. We are working with large clients with hundreds of apps and baking them all into
a single gold image isn't feasible. 
App-V native gives us the capability to target users easily and not have to provide an extra config for masking shortcuts (AppSense etc). It's the whole publish to user, stream down, cache to persistent drive (for other users) in a timely fashion that's
driven the decision. 
Hope that makes sense. 
David Murphy

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