Something everyone seems to be vague about is the fact that anytime you do anything with any of the images in the root/images folder the images are not over written but kept and the filename appended (with -01, -02, etc.) every time you change the image.
There are various threads that discuss this "phenomena". Here are just some...
http://forum.x-cart.com/showthread.php?t=25120
http://forum.x-cart.com/showthread.php?t=54176
http://forum.x-cart.com/showthread.php?t=51189
What we do is upload the images to a sub-folder we made in root/files named images_backup with the same sub-folder structure as what is in root/images (i.e folders named T, P, D, M, W, C). Then we upload our images there and "point" x-cart to them.
This can be done via .csv file or manually on the product modify page in admin.