RSM is what Naruto gained from the sage, he did not lose it, now the tail-beast cloak that he got is different but it's subject to change depending on his attire. RSM is noted for lack of pigmentation and his skin doesn't glow with chakra unlike average BSM or KCM. So no, Naruto didn't lose it, on a plus side, Naruto was winning against kaguya because he had the ability advantage that sasuke didn't have, senjutsu, as shown against juubi jins, senjutsu is the most effective against them as the senju tree is nature a d senjutsu involves nature, fight fire with fire right?
Same thing goes if Naruto was facing an opponent that could only be beaten by a rinnegan then sasuke would have the advantage, in fact right now only Sasuke van trace Kaguya due to his rinnegan, both have pros and cons that compliment the other. During IT only Sasuke could resist it due to his rinnegan another point just putting out there. And yes in the end Naruto won, but you're selectively reading it, that was wind release rasengan not standard Naruto didn't train all those years with jiraya to just go back to standard, wind is super effective against lightning so if sasuke went in with chidori his chidori would get beat due to naruto's elemental advantage. However, fire is super effective against wind which actually evens out Chidori's weakness making them equal and both were amplified by kurama's chakra as kurama gave Naruto the last of his chakra to fight sasuke, elementally they were equal, wind super effective against chidori but weak against fore and both kurama enhanced, it was balanced. They both fought valiantly but Naruto had a stronger will to win than Sasuke so physically it was a draw but ideologically Naruto eon. Same for Sasuke, if sasuke had a stronger drive to win he would've analyzed the situation more in depth and stop reveling in his rinnegans power that he hasn't even mastered yet with those two he would've won. It was a battle of wills that kishi was trying to display I don't see why fanboys have to ruin such a great battle by trying to put the opposing person down, they both fought equally great.