After in-depth analysis from the developers, I have some information to share. The short answer is everything seems to be behaving as intended, given the state of your website before the relationships migration. The reason there appear to be duplicates has to do with the fact that the Partnership posts were not marked as translatable. Here is a more detailed technical explanation from our developer:
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I'm going to use the specific example of post #6936 ("Photothèque de la Ville de Luxembourg", FR language).
The post has two translations with the same name, that together make this translation set:
#6936 ("Photothèque de la Ville de Luxembourg", FR language)
#6940 ("Photothèque de la Ville de Luxembourg", EN language)
#6941 ("Photothèque de la Ville de Luxembourg", DE language)
Each of those posts is connected via (legacy) post relationship to a different post of the partnership type:
#6936 --> partnership 6942
#6940 --> partnership 6934
#6941 --> partnership 6943
The partnership post type is NOT translatable, so each of the partnership posts is seen as a completely separate element.
This whole situation is possible because of the fact that the legacy implementation didn't care about post translations, it sees every post separately.
Now, imagine that we perform the migration.
The new implementation behaves differently: Practically speaking, we no longer connect posts, but translation sets. This has to do with the fact that we store associations only between posts of the default language ID (of course, all this is true only for translatable posts).
When migrating, all existing connections to posts that are part of a translation set (all our "partner" posts from this example) are now connected to the translation set as a whole.
That means, the translation set (#6936, #6940, #6941) now has following associations:
(#6936, #6940, #6941) --> partnership 6942
(#6936, #6940, #6941) --> partnership 6934
(#6936, #6940, #6941) --> partnership 6943
The situation would have been different if these "partnership" posts were also translations of each other, in that case, the migration would produce a single association:
(#6936, #6940, #6941) --> (#6942, #6934, #6943)
So, the conclusion is that everything behaves as supposed to, but the site's design is not optimal. The "partnership" posts should be translatable and correctly linked before running the migration.
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So it looks like there is no bug to resolve here. Let me know if you have any follow-up questions and I will be happy to relay to the developers if necessary.