You will NOT need to delete any of your previous manifest files from the FTP _INBOX.
When NetGalley processes the manifest files that you upload to the _INBOX at sftp://ftp.netgalley.com, the files will be discarded automatically, allowing you to upload others. Please take note that we process these files once per hour.
Here's a tip: add NetGalley to your internal workflow to manage which titles are being added to NetGalley.