If you want all 3 choices to be seen for choose_yes, remove if conditions from All other choices except 1st,like
"1st choice"if(choose_yes) {
}“2nd choice”{
}“3rd choice”{
}
With your current code only one choice the 1st one will appear if choose_yes is gained. And the bottom two choices will seen if choose_no is gained previously. If this is what you are going for and the problem is there, close the respective gain flags under story modifiers and clicking on restart Episode would help.