Application.cfc will not be affected by an Application.cfm in the parent folder. You should replace the Application.cfm with an Application.cfc and then in your child folder you should extend the parent Application.cfc. This is the way the Application framework in ColdFusion functions.
That said, if you cannot replace the Application.cfm with an Application.cfc then you could break out the session variable definition into a separate file and then cfinclude it into the Application.cfm and repeat that inclusion in the Application.cfc in the child folder. However, you may have other things in your Application.cfm that will also not be included in the Application.cfc in the child folder so this isn't really a great solution. The best solution is to get rid of the Application.cfm altogether, replace it with a proper Application.cfc in the root and then extend that from any child folders as necessary.