Nowhere in the Constitution is there any specific authority given for Congress to repeal, although it's been done quite a number of times throughout American history, presumably on the assumption that the legislation being repealed concerned matters within the scope of Congess' constitutional power, and therefore the repeal was also within that scope of power.
But (de facto) repeals of earlier legislation deemed to be unconstitutional have traditionally been done through court decisions, not through Congress. So there could be a problem citing a particular clause in the Constitution as the basis for repealing, say, ObamaCare, because ObamaCare itself cannot be supported on any Constitutional basis. There's the dilemma.