JK> Does anyone know the difference in meanings between
JK> kilesa and uppakkilesa? The dictionary definitions
JK> suggest defilement or impurity for both. What
JK> subtlety of difference does the upa- prefix bring, if
JK> any?

On the second glance, I think that besides the tinge of 'on, upon',
there's also a shade of 'coming close from down under'. That is,
'upakkilesaa' are considered to be somewhat lower, or secondary,
adjoining, to those things on which they appear.

Simplification 'kilesaa' loses that shade.

Metta,
Dimitry