I have a cel too that is covered completely in
black over the paint.  I think they intended to
make the character appear that he is in the dark
and rather than having to use a whole new line of
colors and shades, they just used the same colors
and covered it in black to make it a few shades
darker.  I am not sure though as I am no expert as
far as how they paint cels.  But, all I can say is
that I have also seen this done before.

Star Phoenix