As I already suggested, your requirement is very unusual. I went through following website for Philippines's VAT laws.
But, I didn't came across anything which suggest following:
compute VAT from discount
Whereas, it is rather contradicting, when you state following:
to present in accounting document theNet Value of Discount from 12% value added tax
In my opinion, I would interpret that as Tax on Total Net Value after Discount. Rather than VAT from Discount. And for that, Lakshmipathi Sir already proposed the solution.
If you feel there is still confusion or concern on this. Then I would suggest you to check & get clarified with people from your client's business side for this requirement.
Best Wishes, JP