Lewis, sorry to ask you to double confirm because this is very very important for me, too. thanks thanks thanks!
My experience tells me that it is impossible for any school to check out the specific item in one's application package before making the final decision. Again, it is what I have learned from past one year application experience.
This is my concern too. We've always have to make two-hand preparation.
To make up for the lack of recommendation from my direct supervisor, I'm asking a regional head (indirect supervisor) to write it for me (in confidentiality). She may not know me as well as my boss, but should still be OK.