I had spent a good two week troubleshooting issues with Blender export and UE4 import in search of a good workflow. As far as I’m concerned, such a workflow does not exist. I can bring custom meshes and animations into UE4, but there’s a bit of witchcraft involved to sidestep some bugs that are making fbx import less than smooth.
Upload your trouble animation. I’m guessing you are keeping separate files for your skeletal mesh and your animations, so a blend file for each animation and one for the skeletal mesh. In truth should be asking for the mesh and the animations, but I have a hunch I won’t need them.