This is really cute and unique :)
I don't know a ton ? about clip studio paint, but with other programs you usually need to:
- Merge all the layers together. (If your program doesn't know how to do this, saving the full size as a png and then opening that file will be a merged file)
- Then resizing. If your file is more than 2x the size of the final, then I suggest resizing it to the 2x and then the 1x. (So if it's greater than 250x500, resize it TO 250x500 and then down to final size of 125x250.
If neither of those suggestions help, then it may be a clip studio issue unfortunately.