Dear Aspirant,
First of all you don't need to worry. Since you have opted YES for fee waiver you need to produce the required documents for verification. According to me you can provide a proof that the income certificate is in progress by showing a receipt or any particular evidence but this is not the correct way so I would recommend you to contact the help center on that particular website or you can contact the officials for this matter. Also your Father's income certificate needs to be fast-tracked.
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