If I consume my 30% Shop Discount will it disappear from the legacy site?

Yes. I ended up buying two - one to keep locked in my inventory on the legacy site and one to get consumed on Kumos.

Oh snap. Thats not ideal. I suppose I will wait to see if it is ever integrated together.

might as well just hold onto it as-is for now, until all shops are permanently moved to kumos and that becomes the only option.