Hi Muhd,
I assume that you are granting quotas to employee using RPTQTA00 program since you are not using time evaluation.
Granting quota through RPTQTA00 is equivalent to creating records in IT2006 manually.
Since time evaluation is not being used, there is no way for the system to calculate the no. of absence quota accrued since the start of quota till the termination date.
Hence, the current practice of manually changing extra leaves taken to unpaid leave is the right one.
Thanks and regards,
Vivek Barnwal