Are you looking to avoid PitStop to make the fix or not finding the fix in PitStop, so you're looking for it in Acrobat?
Once you have rotated some of your pages, manually or using a PitStop Action, you can Normalize Page Rotate Key at the end of your Action List or as a separate one. This will remove the rotation key so that no matter the orientation, the key will be zero. Also, if your imposition software honors the rotation key, you have some pages 90° from the others. I hope that I am understanding your need clearly and that this helps.
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