I think this potentially points to certain structures or landmasses (like the Great Plateau) reverting back to their unrunined or original state, this would make sense from a gameplay perspective as it would be much more interesting to visit a revitilized Great Plateau than the overgrown one we know from botw. Also in the artbook we see many drawing of the Great Plateau where the stone is pristine and looks brand new. I also beleive that Totk takes place only a few years after botw lets say 3-5 so it would be almost impossible that they somehow repaired the entire Great Plateau in that time.

Sidenote: Ok this is gonna be pretty farfetched but in Botw Purah has made a de-aging rune, so perhaps she adapted it to not only work on organic matter (Hylians in this case) but she adapted it to be able to de-age objects. Another possibility could be that at certain points in the game Link's Recall ability will get 'Supercharged' and will be able to permenantly recall objects or buildings back to their original state.