I can only tell you how my situation worked out
My Rottweiler is highly dog aggressive (but lives in a multi dog household). When my female Tori went back to the breeders to have her litter I had no issues with bringing her back home. My Rottie seems to be great as long as my scent is still on Tori, or any family member dog can come over with no issues. We have tried to figure this out, but, gave up! Are you able to visit your JRT while away having pups? can you take your Dobe with you for some hikes together (mom needs time away from pups)...I did this as well, I picked Tori up in the morning and took her and my other dogs for a walk. It was great for her to get away from the pup's...and it gave the breeder a chance to handle the pups etc.
Have you worked with your Dobe and tried some desensitzing tactics? You might want to purchase a basket muzzle for reintroduction. And make sure you go pick up your JRT with your Dobe in a neutral area....that way they can get reaqainted with each other without the home territory issues in the way.