Memoria.FFPR
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KB: Importing atlases can changes the size and position of sprites
The problem arises when the rect of the sprite do not match the rect of the texture fragment.
For example: Sprite Rect: 48x48 Texture Rect: 35x35
Such sprites cannot be created at runtime, only in the editor. Because of this, the pivot and the size of the sprite are changed during import.
There doesn't seem to be any way to support for replacing such sprites, except for repackaging bundles.