Thanks @jgonzalez
Actually everything seems to be working fine now (yay) after a clean FBX import from scratch and setting up all the animation parameters and masking again. So I guess internal data had eventually gotten corrupted in Unity. I’ve done the “copy/replace in explorer” update a few times and issues haven’t returned. I guess I’ll just keep my eyes open.
I’m using 2017.2 (forced to collaborate in a team). The mesh vertices are less than the limit, although the total Blender tris are > 65,000 (which worried me for a while). I export by selecting the skin mesh(es) and armature, then export “Selected Objects” Empty+Armature+Mesh.