Dear Travel Dream,
I'm terribly sorry for what happened to you. It's really awful.
I'm not asking you not to be mad and frustrated, but I'm asking you to look at the bright side that your NOC is still has long way towards the CAP.Thanks GOD that you still has the chance.
In my opinion, sending or not sending a letter of explanation will not make a difference in your case. (It would may make a difference if your NOC has reached the cap as in 1122).
After all it's your decision to write an explanation letter or not.
But i would really advise you to change the way by which you had represented your file the first time.
Try to make it more clear, representable and attach a paper writing (as a summary) what all documents that you have sent this time.
While you are doing this remember Allah's mercy that:
1- Your chance to the cap is quiet good.
2- Your file is returned after all and not lost.
3- This hard way that we are sailing through is so hard for all of us (by different degrees) so that we'll appreciate at the end the ripe fruit we'll get.
Good avisesand suggestionmmay
Trust in God.
My prayers for you.