So, I’ve been fighting this too. Trying to export a skeletal mesh to Blender, then export it from Blender so it can be imported back into UE4 and work with the existing animations.
There are a few issues that get in the way. Some of them are solvable, some I don’t think are with the current FBX Importer and Exporter in Blender. I’ve come to the conclusion that something in the Blender FBX Importer or Exporter messes with bone orientation. This issue has been raised with the Blender foundation, but the tickets I’ve seen all have a comment in them from the Blender developers along the lines of “this looks like a problem with UE4”. Of course, it’s not, because no other 3D package has this problem.
So, anyway, here are the issues.
First, Blender imports the root bone as the armature object. You’ll notice that the Armature (not the Armature Object) is called Root, and there are three root bones. UE4 can’t handle three root bones; it requires one.
This problem is relatively easy to fix. You can add a new root bone and name it “Root”, then parent the three existing root bones to the new parent bone. That will solve the hierarchy issue. However, if you export the model, the animations will be all wacky, with limbs flying around through space.
I’ve tried every set of import and export options and have yet to find a way to work around this. There are, however, two workarounds.
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Export the model, but import it into UE4 and have it then create a new skeleton for the model. You can then use animation retargeting to copy existing animations over to the newly imported model. I find this doesn’t always work, however. Sometimes, you get the same weird flying limb animations.
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Export the animations from UE4. Import them into Blender with the same import settings as you imported the model. The animations will work in Blender, but you’ll have to do a little work in order to be able to export them. First, you’ll need to make sure that the Action’s armature name matches the object being exported. Typically, when you import the animations into a file into which you’ve already imported [FONT=Courier New]HeroTPP.fbx (or whatever file), the new one comes in as a new armature with .001 appended to it. You need to manually change that to match the first one you imported in. You can delete the skeleton that gets imported - the action will stick around because they default in with a fake user (“F” button). You also need to make sure that you add the root bone and parent the three existing root bones to it. Finally, you need to make sure that the root bone has keyframes in the action. The easiest way to do that is to bake the action. That will create a new action with keyframes for every bone.
Once you’ve gone through those steps, you should be able to export the model and animations from Blender and UE4 will import them properly. You will either need to rotate the armature object 180° on the Z axis (Y axis in UE4), or else in the import settings specify a yaw of 180°.
Here’s hoping the Blender foundation eventually accepts that this is their problem and fixes it. Until then, it’s a heck of a lot more work to use Blender for skeletal meshes than Maya or 3DS Max or, frankly, any program that can use the official FBX SDK. 