Remnant can regenerate or at least stop further permanent injuries from being made to somebody, knowing Afton, he most likely attempted to get more Remnant to heal himself (alongside using spare parts in Fazbear's frights to fix himself) but it was unsuccessful, leading to Scraptrap not only having more humanoid parts but a distorted version of them plus having parts like feet again. After being burnt a second time, this would have gone out of the window and all of that progress would be lost. I assume Vanny fixed him somewhat
