I've been able to track down add-ons for batch Obj import and batch STL export but I can't find one for batch STL import. Does anyone have a link to such an addon or have a python script?
Start with importing obj file:
Then you export the scene with
bpy.ops.export_mesh.stl : doc
After doing this, you need to delete all instance inside your scene and loop the process again. Should be a fairly easy add-on without tricky point.