Sorry Vinod is right. exempted goods are part of bill of supply. you have to issue different invoices in this case. Tax invoice for taxable and bill of supply for exempted
Govt has told in the twitter that shop sellers can issue a tax invoice for both taxable and exempted supply ( but this option is given only incase of B2C sales ). refer Q.No.45 in the attached regarding the same
In HSN summary it asked for taxable value.. But excempted supplies are not taxable at all... So, I think only quantity is to be taken and the rest remained nil