This code works fine: message.setAllNodes('GT1[@6.1=(000)000-0000]-6', '');
This code only blanks out first occurence:
var i = 1;
var pid13Count = StringUtils.splitByWholeSeparator(message.getNode('PID-13'), '~').length;
for (i = 1; i <= pid13Count; i++) {
message.setAllNodes('PID[@13.1=(000)000-0000]-13[' + i + ']', '');
}