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Rule 6 of CCR2004 says about the Obligation of the manufacturer when manufacturing the dutiable and exempted goods. There are three option
1. To maintain the seperate account for Cenvat Credit
2. To reverse the cenvat credit to the tune of the exempted goods cleared
3. Or to pay the 5% value on the clearance value.
In your case, it is seen that you are not maintaining the seperate account for dutiable and exempted goods.
It is better to pay 5% of the clearance value of the exempted goods. This will the debit from the Cenvat account. For example, if the value of the exemplted goods cleared is Rs 100, then you have to debit Rs 5 to RG account.
This will be cost to you where as this is not going to charge to the Customer. This value doesnt reflect on the Excise Invoice hence the Credit to the Customer will not be possible.
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