Yes, a list with a New-List= keyword still uses points based on how many
users are left on the list when you set it.  Normally you should do a
QUIET DELETE listname *@* before setting the New-List= keyword on a
server with a graduated LAK (obviously this is not an issue if you have
an unlimited LAK).  In any case a list with 0 subscribers will still
use one point.

What you should be able to do in this case is GET the header for the
OLD list (even though you can't get the entire list or perform any
operations against it, you can still GET the header), remove the
New-List= keyword, and then PUT it back.  This will restore the list
to its original state, you can then do the QUIET DELETE, and then
you can put the New-List= keyword back in the header.

Alterately you could just delete the OLD list and create a new header
for it in the usual way.

Nathan