Provisioning Existing site with selected SharePoint objects

If it was just content like that, maybe look at a content migration tool otherwise with PnP you do have the option with the ProvisioningTemplate to specify https://github.com/SharePoint/PnP-Sites-Core/blob/master/Core/OfficeDevPnP.Core/Framework/Provisioning/Model/Handlers.cswhich only apply certain elements to the site, i.e. Lists, Files, Pages and in your site provisioning XML template, update the section for <pnp:Files /> section for what should be added. You could also look at creating a custom extensibility handler for the PnP provisioning framework.

I heard the latest version (https://dev.office.com/blogs/PnP-May-2017-Release) of the PnP CSOM Core and Provisioning engine, the base templates have been updated to be used in delta handling, but haven't tested that yet.

Thanks