It's actually pretty simple, you just need to loop through the main list once and remove item if it's in another list. Here is an example:
clear list(%LIST Original)
add list to list(%LIST Original, $list from text("item1,item2,item3", ","), "Delete", "Global")
clear list(%LIST Substract)
add list to list(%LIST Substract, $list from text("item1,item3", ","), "Delete", "Global")
set(#LIST Original Row, 0, "Global")
loop($list total(%LIST Original)) {
if($contains(%LIST Substract, $list item(%LIST Original, #LIST Original Row))) {
then {
remove from list(%LIST Original