Thank you for responding! Reading the discussion here, I can think of another solution similar to what Tim mentioned :
In the popup window, display the unshuffled question number in front of question number. Add another string below it, say, "Appeared to student on number 4".
So 2 strings (Eg. original question 10, it appeared at no. 4 to a student) :
Question number 10
Appeared to student on number 4
Also, I have submitted the patch for unshuffled question number to appear on the bug page. But I think I'll wait for a final behaviour which everyone agrees upon.