When you use any of the transformation tools such as Scale (S) or Rotate (R), the effect is permanent once you save and close the document. For example, rotate an object, save the document, and close it. Next time you reopen the document, there is no easy way to undo this change. Instead, consider using the Transform command under the Effect menu. You'll find it here: Effect>Distort & Transform>Transform. In the dialog, check the Preview option and then apply whatever transformation you like. Once you've clicked OK, you'll always be able to access and edit these transformations (even after closing the document) by selecting the object, looking in the Appearance palette, and double-clicking on Transform.
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