Unless you're combing multiple files into a single puppet, you're likely better off doing the grouping in PS or AI. Ch Beta 5 (released today!) is better about preserving changes across structure changes, so make sure you upgrade first.
Also, by doing structure changes (i.e. grouping changes) in PS/AI, you'll see the same hierarchy in Ch. Grouping changes done in Ch aren't reflected in the .psd/.ai file.
You can import as many PSDs / AIs as you want, and can drag them together to create a franken-puppet of sorts. So I could have and eyes.psd that I mix with a mouth.ai on a bird.psd. This is even easier now with the new shareable puppet filetype.
Also, for the original question - grouping in Illustrator can be weird. I always select the parts I want on the canvas, not the layer panel, and group from there.
I think a great idea for a short tutorial would address how to group and regroup in Illustrator. I watch and rewatch your tutorials to see how you are able to make your groupings work so well, in that they retain their names and become sublayers of the new group. This is not the behavior I get at all, when I group everything transfers to, for example, the + R Eyebrow layer, and the sublayer names are usually not helpful. Enormously frustrating when I am trying to create head turn layers. Please help!
Never mind, I just answered my own question. For anyone else struggling with this, I simply selected all the desired layers by name, and there's an option in the Layers panel called Collect in New Layer, and this takes all your selected layers and drops them into a new layer with all the existing layer names intact.
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