By changing your engraving direction, the dust produced during the engraving process will not be able to settle of the warm, freshly lasered workpiece surface. Instead, the dust should be extracted (depending on what kind of machine you are using) by one of the extraction systems. As a result, the unprocessed part of the material will always be engraved first, so that no dust will be able to land on the newly-engraved surface.
Additionally, the changed engraving direction should help you see the material as it is engraved. By moving backwards, the axis will not obscure your vision. For example, this means if you have a last-minute change you wish to make, it is much easier and quicker to pause the process. This may lead to less damaged or wasted stock.
Stamp engravings are usually done with a standard 'top to bottom' setting. The engraving dust happens to be much heavier with rubber than with other materials and will remain on the workpiece instead of being sucked into the extraction system. Reversing this will, hopefully, give you a cleaner result.