that option allows the use of alternate images, it only works on level 1 and up, the "egg" image or level 0, wont be affected, so you will not know if you got a shiny or a normal, until it reaches the next level. when you add a new level just make sure to put both images, and yes the alt stays through all the levels you create, just remember to add both images, the normal and shiny image.
I hope i explained in a make sense way, English is not my native language.
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