I have a similar problem (using Toon Boom Studio 8.1). In my case, it’s the “scale” of the imported elements that goes haywire once I create hierarchies.
I have a PSD, with separate layers for head, arm, hand, and so on. Naturally, they are all at the correct sizes, with the hand being just the right size to fit underneath the sleeve of the arm, and so on.
When I import them, I have to choose whether to “fit image to camera width” or not. If I choose “yes”, then all objects get a scale of 1.0, and the correct size relationships between them are broken, and remain broken when I start making hierarchies.
If I choose “no”, then the size relationships are preserved, but each object gets a different scale that is relative to the camera. So, the arm might get a scale of 0.27, while the hand gets a tiny scale of 0.08 (because the hand is only 8% of the width of the camera area).
But now, when I make a hierarchy by making the hand a child of the arm, it uses these no longer relevant scales to calculate the new sizes, and therefore makes a total mess of things. For instance: because the hand has a scale property of 0.08, as soon as I make it a child of the arm, it shrinks to 8% of the size of the arm, becoming virtually microscopic. I wonder if this is actually the ‘disappearing’ that the OP was having a problem with.
I get this same problem whether I import the elements as a layered PSD or as separate PNGs.
How can I get Toon Boom Studio to preserve the correct size relationships between objects when I give them parent/child relationships?