my $sql = do {local $/; <>};
$sql =~ s/\( ([^()]+) \) , \n\)/($1)\n)/x;
print $sql;

##</code><code>##

C:\Users\...>perl -i.bak chop-sql-comma.pl CUSTOMER_NEW.txt

##</code><code>##

perl -Mv5.14.0 -i.bak -e^
 "local $/;print <> =~ s/\( ([^()]+) \) , \n\)/($1)\n)/xr"^
  CUSTOMER_NEW.txt