I got 2 deepsight weapons as part of the quest and received progress for only 1 out of 2. Today I finally had a random deepsight Taipan drop and I did not get credit for it again after getting all of the kills to complete it. I got the 300 currency for it but I did not get the pattern again.
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I have the same issue with my Ammit AR2. It's really annoying but I believe it's purely visual. Go try and craft the weapon despite the pattern not displaying it as complete. Although I believe this is only visual, I really hope it gets fixed.