Protocol for checking in on a letter of recommendation more than once? Quick background: I am applying to grad school and asked two professors from undergrad and a current work supervisor for letters of recommendation and they all said yes.  I asked about a month and a half out from the due date, gave them all updated resumes/statement of purpose/any other information or paperwork they asked for. My supervisor got the letter finished rather quickly and sent me an email to let me know. About two weeks out from the application due date I sent a brief reminder/follow up email to my two professors ("just a reminder this is the due date, let me know if you need any more information" etc). Last week (about a week before the due date) one of the professors got back to me to let me know she had finished/submitted the letter. The due date for my application is in a few days and I have not heard from the second professor.

My question is: I have already sent an initial follow up email for a letter of recommendation. Is it considered rude or pestering to send a second email? I have no qualms on how to word this email - I will still be very polite and accommodating of course - but I understand professors are very busy. I don't want to be a bother but also I need this third letter of recommendation and this professor willingly agreed to help me. Is there a protocol for a second round of follow-ups for letters of recommendation?
No, it will probably not be considered rude to repeatedly ask for a letter.  The professor agreed to write the letter and clearly understands what it is and why you need it.  If it is a few days before the due date, they haven't turned in the letter and they haven't responded to your last email, they evidently need the repeated reminders.  I honestly think it is more likely that they will be sincerely grateful that you are helping them to complete a task they agreed to do than that they would be even a little bit annoyed with you.  But if they do get a little bit annoyed with you -- okay, maybe that's what helps them write the letter.  It would be highly unprofessional to respond to this kind of behavior from a student by writing a worse letter or not writing it at all, and I honestly don't know of any professors who would behave in that way.

Finally, let me say: faculty turning in letters late is such a common thing that in many circles at least there is a de facto grace period for faculty to turn in letters which is up to a week or two after the actual, posted application deadline.  As a student it is hard for your mind to really be eased by knowing this, I expect, but it helps to understand the faculty mentality: if I turn in a letter two days after a deadline, I would actually be annoyed if it were not considered.  (And I would know it was my own damned fault, but I would be annoyed anyway.)  

Good luck, and keep at them.