One good way to handle this is to add a date/time into the file name.
For instance:
Instead of IMG_1234.jpg, have the file renamed to IMG_YYYYMMDD_1234.jpg.
- instead of IMG_1234.jpg, have the file renamed to IMG_YYYYMMDD_1234.jpg. That way if later down the road you have another IMG_1234.jpg, the exported versions would be dated. So if the images were shot on Feb. 14, 2010 and Jun. 30, 2011 you would end up with IMG_20100214_1234.jpg and IMG_20110630_1234.jpg.
In Lightroom, there are filename templates that can simplify this process.