The problem is that their system has a glitch and their reports have started including some parts that I have already shot and there are images on their server for. Not sure how long this has been going on or what scale we are talking but I am shooting the same parts more than once.
Do we assume that the report shows the correct images and descriptions, just that you have already done those images. The issue seems to be identifying the fault and from what you have described the fault seems to be the report from the db is producing incorrect information? So the report search criteria is wrong or the search pattern needs to be deleted and re-created. I am not so sure that trying to re-process the whole set of images is going to resolve the issue and the fault needs to be resolved before you decide what to do about the contents. There doesnt seem to be an issue with the work you have done so the db needs to be corrected first then decide if the data integrity has been compromised.
Congratulations on your new DSLR a good camera, what lens are you using? As I understand the DDP and PSE software. DDP is designed specifically for Canon cameras so it makes sense from a work flow point of view to use DPP to upload your images from the SD card. Altering images after uploading can be done using PSE or Gimp although I am not familiar with Gimp. Good luck.