SEC - Secondary Site
MT1 - Child Primary Site
Pictures below show on SCCM Child Primary console that Computer Collections and Native SCCM Central Site Software Deployment Packages and Advertisements are locked out.
Here is the procedure how to remove MT1 SCCM Child Primary Site from its MTS SCCM Parent Site.
First step is to delete MT1 child site address from MTS Parent Site via SCCM console.
Next step is to execute Preinst.exe which is located in C:\Program Files (x86)\Microsoft Configuration Manager\bin\i386\00000409 folder:
Delete jobs for MT1 site: Preinst /deljob MT1
Finaly you can see that all locked out items have been removed. All Software deployments packages, Advertisments, OS deployment packages, and Task Sequences have been inherited form SCCM Parent site into SCCM Child Site and can be modified.