Aseprite upscales well.
Would you like to describe your process?
Typically, the best upscaling is by multiples of a hundred: 200%, 300%, 400%, and so on. I’ve read downscaling works best with the default Nearest Neighbor option by divisions of four: 75%, 50%, and 25%.
I’m going go post this next part here not because I think it’s what is happening, but because I wish someone had told me two years ago— Undoing what you’ve already upscaled after an original is lost should reverse what was done, but that can be messy. An example is that 33% after 300% might not return the image exactly. Using the original image for scaling each time is best.