Solved
After code deployment to AEM, jcr:primaryType gets converted to nt:folder from sling:folder
We have this structure, /conf/<appname>/settings/wcm. In source code we have jcr:primaryType: slingFolder for <appName> and for settings folder. But when this code gets deployed to AEM, jcr:primaryType is getting converted to nt:folder instead of sling:folder. Any pointers will be highly appreciated.