For Pokemon that can only be battled once (such as Giratina or those delta Pokemon), instead of disappearing forever, a tesseract spot should take their place to let the player rebattle it anytime until it’s caught.
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…That’s BRILLIANT!!! It isn’t even just a random deus ex machina of them deciding “you know what, I know that I was only able to show up their because I was summoned in this really specific way, but I think I’m going to go ahead and go back and appear in the same location as before with no logical explanation as to how I achieved that powerful form without other-dimensional space magic or ecological necessity”, but can actually be justified in the fact that we are literally traveling back in time to battle them again.