For your non-moving group, I think it would be better setup as this:
You should also setup your group boundary to be the full width of your document – this will keep its sizing at a specific ratio of the available width.
For the moving Red element, it may not have been appearing because individual elements within the group were set to scale – this may have had the effect of making the elements have a 0 width and height so they were effectively invisible. Setting the flex layout properties just on the higher level groups in your document should result in more dependable effects.
bigwig_logo_anim-red2.zip (42.9 KB)
When publishing to Indesign, the frame in which your Hype document appears is also scaled down – this might have been what was making the initial text disappear.