To remove a folder or file you have added to Overdrive you will need to delete/remove it in Google Drive. Open the Drive folder and move the file outside of the Site Folder. This will delete your page from the Overdrive site.
To hide a folder or file from all site users, go to Page Settings > General and uncheck the Folder Contents box under Page Visibility - the selected folder or file will no longer show in folder contents. You can also hide a page from the menu by unchecking Top & Side Menu.
Page Administrators can view any hidden folders or files in a Folder Tile by clicking on the advanced filter arrow and choosing Show hidden files.
Instead of hiding folders and files you can use the Overdrive Permissions tab under Page Settings to only show a particular folder or file to selected Groups. You can also use Google Drive permissions to limit what users can see. You will need to make sure the site Discovery is set to Google Drive in Site Settings, then Overdrive will only show a user the folders and files they have at least View Access to in Drive.