There's certainly no way of doing this automatically. I don't understand how your scene is set up at all right now: how do you have separate reference meshes but not separate flex exports?

If you're trying to use flex shapes you created with one mesh on a different mesh, that will never work. The verts would be totally distorted in the compiled model.

This has nothing to do with the export format. The issue is that you're trying to export a vertex animation but your scene doesn't have a rigid body world. You need to either create one from Scene Properties, or remove your vertex animation(s).

I'll fix the error for the next release, as it should be possible to do the export without the rigid body world.

Shape keys are listed in Mesh Properties.

The only other names that are exported to SMD are those for materials (or per-face textures).

You have one or more shape keys with bad names too.

The error is that a character in the name of a bone can't be converted to ASCII. You should check the names of each one to make sure that there's nothing strange in any of them.

The easiest way to do that is by changing the Outliner to Datablock view (it's probably "All Scenes" right now), then expanding Armatures > your armature > Bones.

Are you trying to export an object with a name that contains non-English characters?

Hi, you need to go to the Scene Properties panel and set up the export. More details here.

Sorry about Vintage being a dick. I've banned him for a while.

You need to enable Advanced flex properties. Provide the original demo_morphs_high.dmx file as the controller source and the wrinkle maps will be generated for you.

It's impossible to tell what's gone wrong. Could you list each step you took, please?

Not at all, it's difficult to tell what's gone wrong from the error unless you know how the addon works internally. :)