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I'm not sure if I understood it correctly. The duplicate check "Update Previously Added" works when a previously added submission using the zoho receives the same data submitted, this will update the same submission done, but this is only by my personal knowledge.
But please do try the following workaround below. What we will do is edit the submission (the existing ones that you have in Jotform but not in Zoho) and re-submit it to update it in Zoho. You can follow the quick guide below.
1. Navigate to "My Forms"->Choose a form->Click Submissions
2. Choose a submission that you don't have in Zoho or you want to update, click the "Edit" icon on the right.
3. Update the field values and click the submit button.
Please check if the submission was successful in JotForm and in your Zoho setup.
If you are still having problems, please also do try Zapier App for JotForm and Zoho.
I hope this helps. Let us know if this works.