Okay, so I've been working of trying to unlock the Pattern for the [armory]Taipan-4FR[/armory] Linear Fusion Rifle with 1/2, and I just needed to get a second one to use the Deepsight Harmonizer consumable on. I finally got one as a drop today, and immediately used it... though the one I had just gotten was a bit higher power than the Masterworked one I already have with perks I preferred to the new one. I knew you could dismantle a weapon to extract the Pattern progress as well, so I thought, "Hey, two birds, one stone."
Then proceeded to dismantle the new one with the Deepsight Harmonizer applied for infusion with my Masterworked Taipan-4FR.
And it only raised the power level. The Pattern progress was not added, and I have no way to get that Exotic consumable back. So that... really sucks. I assume this is a bug, and hell, it might have been due to me infusing it with one I had already extracted the pattern from. Couldn't say. Either way I'm just kind of at a loss on what to do about it.
TL:DR - Don't disassemble a weapon for infusion before extracting Pattern progress if it has Deepsight Resonance. You screw yourself out of that progress.
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Dismantling for infusion has never granted any materials, reputation, or pattern progress as you are transferring the power to another weapon. They updated Deepsight so that you don't need to equip/use a weapon in order to extract the pattern progress.