Unfortunately this is correct functionality at the moment. Leaving the game prompted the scene to reset, possibly because of a power saver feature on your device. This closes all of the open windows in the game, and so refunding the scroll in this case would make it easy for players to exploit that and keep the scroll of the metamorphosis options shown to them weren't what they were looking for.
Pixel Dungeon
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Ok, next time I will be careful then... Maybe i will put it on airplane mode first!
Dungeon Crawl Stone Soup had a similar issue with scrolls of acquirement. They solved it by remembering the selection of items offered by the last scroll read and re-presenting the same selection every time. Since the selection is global, you would always get offered the same items even if you read a different scroll of acquirement.
This had the side benefit of allowing the player to read the scroll, decline to choose an option, and close the scroll without wasting it, knowing they could always re-read the scroll and get presented with the same options as before.
Perhaps this solution could also work for scrolls of metamorphosis. One catch might be that you’d need to prevent the player from using that scroll in alchemy as a way of avoiding the choice altogether and recouping the resources of the scroll.
Or perhaps another way to do it would be to store the scroll’s options in a buff that keeps re-opening the window until the player has made a selection and then remove the buff afterwards.
I have actually decided to look into improving how some windows persist between scene resets, but I don't plan to put in full tracking functionality so that the scrolls window will re-show if the game is closed. I'd rather just treat that as cancelling the scroll given that in most cases you have to force quit the game for that to happen.