[b]Edit:[/b] Bungie confirmed in the [url=https://www.bungie.net/en/Explore/Detail/News/47602]1/31/18 TWAB[/url] that this bug is known as part of 2.1.4. It is also known that the Sniper frame in question can potentially disappear from your inventory after logging out.
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Fallen are not dropping any Compound Ether to progress the Black Armory basic sniper rifle frame. Specifically, this is the frame you get as a drop from Ada-1 after unlocking the Gofannon forge on Nessus.
From reading some guides online, when you're on this step of the frame, any Fallen should drop Compound Ether on any kill, anywhere. It's also supposed to drop fairly often (more than half the time). I've tried killing Fallen on both EDZ and on Nessus, with headshots, with a Black Armory sniper rifle, etc etc, with zero Compound Ether dropped. After asking around on a couple Discords this definitely seems wrong.
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As of the 2-6-2019 at 11:00 CET the issue is not yet resolved and my sniper rifle frame has disappeared upon logging off