No. The File Manager and the Legacy File Manager show the same directories and the same files within those directories. It is not possible that they would show you two different sets of files. The two interfaces are just that - interfaces - that show the same data.
Before doing anything else, clear your browser cache. Web browsers cache many pages and this can make it appear that a change has not been made, when it has, or that something is not working, when it is.
Your hosting provider should be able to help you with this, if clearing the browser cache does not help. Your hosting provider has direct access to your site, which we do not, since we do not actually host any sites or servers.