If your cookies in same format as BAS, you just read it from file to variable and go Network-load cookies-set cookies for browser. If format of your cookies not compatible with BAS, compare and convert all your cookies in right format
If you want the second folder to stay updated with the potential changes that appear in the original folder after working with it, then yes, you would need to copy it again.
open website
execute javascript on the page to delete all cookies for the page
function deleteAllCookies() {
var cookies = document.cookie.split(";");
for (var i = 0; i < cookies.length; i++) {
var cookie = cookies[i];
var eqPos = cookie.indexOf("=");
var name = eqPos > -1 ? cookie.substr(0, eqPos) : cookie;
document.cookie = name + "=;expires=Thu, 01 Jan 1970 00:00:00 GMT; path=/";
}
}