I’ve got a simple flapping bat that I’m using as a particle instance, is it possible to emit smoke from these instanced objects?
From their center point, probably yes, from the instanced mesh surface, maybe no.
If you need to emit from the surfaces, try exporting your instance bat animation as an Alembic .abc and then import that for use as a smoke generating surface.
If what you mean by particle instance is unique mesh object using Particle Instance modifier before Fluid modifier.
That should work.