What makes you believe that this part of the constitution cannot be amended? Article V only says that it requires consent of the affected states - which would be all of them, so it's a high bar, but it's not outright prohibited.
That is a very interesting question. One could argue that the spirit of the clause necessarily implies that it cannot be amended itself without consent of all states.
Another possibility would be to nullify the powers of the Senate. So all states would still be entitled to an equal representation, but it's in a body that is purely decorative, so they're welcome to it. This is also arguably counter to the spirit of that clause - although that would be more difficult to argue, since the power of all states would be equally diminished...
But either were to actually happen, the question would rather be, to whom would you make that argument, and what power would they have to enforce such a decision anyway? I would dare say that if anybody got the supermajority necessary to amend anything, they could just roll with it and disregard any objections - just as they disregarded all those who considered the Constitution illegitimate, on the basis that its ratification didn't follow the requirements set by the Articles of Confederation.
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