I am working on this medieval flail. As you can see in 3dexchange the hierarchy is intact and each link is a separate object.
The idea is each link is its own object to be made into a rigid body. I exported this from 3d Exchange as an iProp and look what happened...

...the separate objects merged into one. I know I could save each link as its own iProp and line them up in iClone but that is too time costly for repeating each time I need to use a flail. Is there a way to keep the hierarchy intact for an iProp? Or a way to add the rigid body to each link in 3d Exchange?

You need to select each object in 3DX and click "Make Sub-Prop" in Node section. Then, they would travel to iClone as sub-props to the root node dummy.

Thanks, the sub-props did the trick. After loading the iProp to iClone I fixed its scale.

::BTW why do I need to fix the scale for my props? I had the handle the right number of inches when I exported the flail from blender as an fbx. Then I opened the FBX in 3d exchange. After doing the work in 3d exchange is saved it as an iProp. When I brought the iProp into iClone it was ten times larger than the size I needed. It seems to me it should stay the same size. I have the human in the background so I could get the scale right. Why aren't humans kept to a realistic size when exporting to another 3d software that works in measurements?  Does anyone know how to do this? Does anyone know how to work in feet and inches in Reallusion? It seems any good 3d software should allow you to work in real-world measurements.::

After that I applied dynamic physics to the ball and all the links. I applied static physics to the handle just as a test (I know I will need to make it animate-able). I made them all self-mesh bound type. When I pressed play the computer took a fairly long time for iClone and the prop became really large.

Picture below to give you an idea.

Does anyone know what causes this? Is there a solution? If so, what is it?

iClone works with real world units - metric
1 iClone unit = 1 cm
Buy default, 1 square of the grid in RL products  = 1x1 m  or 100x100 cm

Now, anything you export out of Blender should have transform reset. If you fail to do so, you might have problems described.
For every object In Object mode:
Ctrl+A > Location
Ctrl+A > Rotation and Scale

It is also good practice to reset scale for all objects in iClone before you begin animation/parenting/physics

Thank-you for that information on units.
I applied the scale of the flail prop and then reapplied all the psychics settings I had before (dynamic for chain links and ball, static for handle.) When I pressed play, the chain links phased through each other at some points and iClone really slowed down and goes into "is not responding" when I press escape to exit the animation. Here is a screen-shot I grabbed of the chain breaking apart. Is what I am trying to do possible in iClone? If so, how?

Don't use self-mesh. You will stall the iClone to a stand-still. Use Convex Hull instead.
Attach everything to a dummy.
Handle is kinematic, the rest is dynamic.
Give chains some good damping ~500-1000 and use point-to-point to constrain them.
Like anything with physics it does require a lot of patience.

Here is typical setup for the links physics:



And Point-to-Point constraint:




The result is pretty much acceptable. Just need to be very careful with animation as constraints can still very easily be broken.

Improvised flail:

Wow, that looks quite convincing!
Would be cool to have a chain like this (a bit longer without the ball)





Toystorylab on Vimeo :     Crassitudes (my "Alter Ego") on Youtube: 

Would be cool to have a chain like this (a bit longer without the ball)

I did not do anything really special here (as the mater of fact the ball gave me most of the problems)

If you have a Hottest Hairstyle pack, have a look at chain necklace accessory.
You may release constrain on one end and have it straight

Thanx for that! (Though it does not work as convincing as your chain does...)





Toystorylab on Vimeo :     Crassitudes (my "Alter Ego") on Youtube: