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                   4825 Points
                   Joined December 2018
                
               
			  
			  
             
            
             Credit in relation to export of goods is clearly eligible based on section 16 of IGST Act. 
MEIS scrip although is an exempt supply, the credit in relation to export of goods cannot be considered for ITC reversal as the credit is directly attributable to the goods and not the scrip, which in turn is fully eligible. 
This may be one of the ways to confuse or harass the assessee, suggest you to go meet with higher authorities to resolve this faster. 
Alternatively, as the law is clear, await for them to raise an SCN and respond to the same.