Hagoromoo only gave naruto and Sasuke the seal, so if they use it on Kaguya it may fade away.
The rinnegan and Sennin mode are permanent because Hagoromoo didn't give that to them.
As long as the cells kabuto gave Sasuke are still there, he will still have his rinnegan.
As long as the Ichibi/Hachibi bijuu piece chakra that Obito gave naruto is in naruto with the others even bijuus, he will still have Sennin mode.
PS: naruto and Sasuke do not have half of Hagoromoo's powers.