Can't say I've tried it, but if the LoC IG2 didn't have it then I guess you just answered your own question. I think for special items, if you already have one of them you won't obtain another one no matter what. You should still be able to obtain new copies of regular R40s that way though.

I leveled/perfected about half of the Special/unique items, and yeah, seems like you can't get copies of them from the IG/IG2. As SleepingSeaweed mentioned, most of them you can't even get multiples on subsequent cycles, though there are exceptions (the only good/noteworthy one being the Usagi's Journal, though it's still a pain to get it).

As a bit of trivia, it is possible to get copies of Accelerators (rank 39 shoe) from the IG, but the rarity is random, even though the Dark Record only list it as being a "Legendary only" item, so you can go (very slightly) above 100% in the item collection.