Hi OP. I would not bother at this point. Unless you plan to ask the same set of references? I would suggest that you seek future references from those who would not be put in a position to use the not observed or 'NOB' in your LoR. To me, an NOB would indicate that your reference is not someone who can vouch for your capabilities - it seems you found this out.
I suggest that when you ask for an LoR, you ask if they can write you a 'positive' LoR. In most cases, those who feel that they don't know you well enough will be forthcoming in telling you why they can't, rather than giving you a neutral or potentially negative LoR.
I had the same issue with my out-patient PT. I asked him for a positive reference and when he checked the online PTCAS reference form, he told me that he will have to put down not observed for some of the areas because he had not had enough time with me to assess those qualities. He said to proceed with a positive letter would be dishonest. I agreed with him. I had only 20 hours with him during that time and over 50 hours with my in-patient PT (my 2nd LoR writer). To make a long story short, I did not have my out-patient PT write me a letter - even though he was willing to. I was familiar enough with NOB marks and knew it may look bad in this situation.
He eventually approached me to write a positive letter but I had already submitted my application at that time. Hopefully, you have had the chance to build a stronger relationship with all your letter writers. Good luck.
