This change only affects the way you see the file in GoodReader. Nothing changed in the file; the margins will still be there if you export the file outside GoodReader. Also, you can
reset the page crops to their original values at any time.
You can also choose different crops for odd and even pages, in case if your PDF file is formatted for binding, with odd and even pages cropped
To crop the pages, open the file and press the Crop button.