Naruto and Sasuke retained their power ups

[Kagustuchi]

Look in the bottom Left Corner of this page. Sasuke still has the Rinnegan after the Seals were gone.

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[saw2097]

Yes, and when Naruto removed his hand from Kaguya after putting the seal on her he still had the mode.

If they were going to lose them they would have disappeared when they lost the seals.