In addition to funding renewals, congress can make specific tweaks at any time to correct anything they dislike with regard to the executive branch. The ruling pretends like this avenue hasn’t existed and been used the entire time.
> I think we will have to wait and see what happens.
What will happen is that anytime someone doesn't like a regulation, they'll now have many, many jurisdictions in which to shop for a judge that will rule in their favor.
Never mind that congress appoints the heads of the agencies, writes the laws directing them, and on an annual basis, renews funding for them.