Ditto. After coming back when i heard of the new expansion and level changes, I too needed to upgrade gems. I was doing that religiously as I upgraded gear. Then boom, it was gone. I thought it was the changing from difficulty levels, but nope. I hope they bring it back and soon.
I think it was intentionally removed because large volume bulk conversions were hindering performance on the server with everyone doing it to remove excess g fragments before they increased the limit.
I also saw the transmute fragments option in jeweler, but today, when I raised a glyph to 45 I don’t have the fragments required and the option is not in jeweler.
I can’t activate Legendary level 45 until collect 140K fragments…
I don’t expect enough people to be preemptively doing bulk conversions, to affect server performance. I expect almost all players who used that workaround to be doing it once prompted by an event. If devs saw otherwise, they could comment on it… but they’re not good at communicating such things, so who knows.
But assuming this is right, then the ‘fix’ (increased limit) should have obviated bulk conversions. If it didn’t, then the ‘fix’ was inadequate.
Also this (below). I still think it was absurd to have gem fragments be a potential glyph bottleneck… but I find it hard to believe the devs had this conversion in place to help prevent such a bottleneck, and then consciously removed it. “Yet another coding/QA failure” still fits best IMO.
The Issue is fixed. 
With patch 2.0.5, is back the transmutation of fragments to alchemist.
Regards