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Are you referring to this form - http://www.jotformpro.com/form/52101577250951? It seems that the Download All Uploads is only limited to 250 MB or 250 files.
You can try to partially download your form (download uploads by batch). You can try to filter it by date and download the form partially.
Basically the idea is similar with this article: How to Partially Download Form Submissions.
Do let us know if you need further assistance.