(TL : DR) I have an idea that might be able to fix this, but I don't know how to do it without a script, or if the idea would even work. Lots of suggestions have been made, but they all involve stripping the controllers off the bones (including the IK and FK rigs that drive the base rigs for the baked animation), unskinning the mesh, exporting weights, and a myriad of other time consuming tasks.

Nobody on the team has a definitive answer for how to fix this. If we scale the master group that contains everything it looks and works perfectly, but when we bake and clean the scene for FBX export we lose the scale on the bones/mesh because the master group is deleted (and the mesh and bones don’t retain that information).

If we scale the rig then obviously the mesh follows, but the controllers for the animators explode. The bigger challenge is that the character is actually a girl on top of a quadruped- so it's not just one rig that needs to be scaled up, it's two. The challenge we face right now is (obviously) that the mesh was never scaled before it was rigged. So when we export the FBX and put it in game, he is too small his scale is 1, and it needs to be 4.8. In essence- our FBX settings are dead on perfect for all our previous characters, but this one character was never scaled in Maya to the size of all of our other characters. Now, the problem isn't the unit conversion method in the FBX export settings, the problem is that the character mesh was not scaled before it was rigged.

We are having a scaling issue on one character we're trying to get into the engine. I am currently working in Maya as an animator for a Unity video game.

Maya fbx export settings for unity