Did you look to see if the missing layers have visibility toggled off in Photoshop or Illustrator?
Can you provide more information regarding the part that isn't visible? Does deleting behaviors fix the issue?
Hi Jerry & Jim!
I ran into the same problem myself where parts of the body and arms disappeared after I did some editing in illustrator. I ended up copying the body back from the template and starting again and I isolated what caused the parts to disappear within the context of my problem.
I am completely new to illustrator so I am not sure what is compromising the integrity of the layers (at least to output for animation) but apparently using the Live Paint Bucket tool in the way that I am is breaking them. Something about converting it to a paint group... I assumed the Live Paint Bucket tool was just a regular color fill tool but I'm guessing it does something a little fancier.
That was a messy explanation so here's a video screen-capture of what I'm doing that's causing the limbs to disappear. It shows what I'm doing and the way the arm disappears after colouring. (Sorry for part of the screen being cut off. I am pressing the 'K' shortcut to get to the paint tool. If you would like me to record the process again let me know)
I thought it might be the fact that the fill causes the sub-layer to change its name from left-arm to 'live paint' but correcting that didn't seem to fix it.
It seems as though my inappropriate use of the paint tool is causing the issue.
Hope this is helpful in some way.
Live paint features in Illustrator don't come into Character Animator, but you can Expand the appearance of Live Paint and have them converted back to fills and stroke. Use the menu command, Object > Live Paint > Expand.
For more information regarding Live Paint Groups, see: