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I presume you want to download your file uploads on your form submissions all at the same time?
Here are the options that you can try:
Option 1: To download all your file submissions, you can check this guide: https://www.jotform.com/help/356-How-to-Download-the-Submission-Files
Option 2: This is an older method when option 1 was still not around: https://www.jotform.com/help/315-Downloading-File-Uploads-in-the-Form-Using-DownThemAll-Mozilla-Firefox-Extension
Option 3: This is the common way to download the submission data: https://www.jotform.com/help/73-How-to-Download-Form-Submissions-as-Excel-CSV-PDF
Option 4: This is a new feature that allows you to backup all of your data: https://www.jotform.com/help/374-How-to-export-all-of-your-data-at-once
If I may also suggest, you can maximize or take advantage of the file sharing and storage service integrations that we have (ex. Google Drive, Dropbox and Box.com), you can check them here: https://apps.jotform.com/category/file_sharing_and_storage. With those integrations, they can automatically upload your file submissions in your 3rd party cloud storage, giving you a real-time backup of your new submissions.
I hope that helps.