Application Reconcile means application students which do payment through cheque, so you can change the cheque status whether it is cleared or pending or bounced.
To open this click on Admin Master --> Fee Payment Reconcile --> Application Reconcile
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Select the class, student Name an click on Find.
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The Particular student will be displayed below with the cheque status.
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If the cheque is still Pending then remain Cheque Status as "PENDING"