Hello Shinde,
The Supplementary Invoice you are talking about, what I think, is nothing but the Debit Memo against the original invoice.
I do not know how you have configured it and why you are saying that double posting of quantity.
Have you treated the Supplementary Invoice "SD document category" as 'M-Invoice' in VOFA?
If yes then you have to treat this as Debit memo category which is 'P-Debit memo'.
Hope this is clear to you. Let me know your point view on that.
Thanks,
Suman