Based on what you describe, this is a complex issue indeed, and an unfortunate intersection of circumstances. I don't think there is a perfect solution.
I don't see a good reasoning to accept the new image unless somehow you can argue that the newer version is better because of either metadata or resolution. You could also check if they have a slightly different angle/version that they maybe did not yet upload to Flickr. These are all imperfect solutions though.
You could discuss among yourselves whether to accept these submissions anyway in the national competition; you have some leeway there - but I should warn you that most likely these images would not be accepted as 'new' in the international competition. The international jury has to stick to their rules, I'm afraid, and I think the definition is pretty clear here, however unfortunate this is for the photographer.
I'm sorry that I don't have a better solution.