Missing Recommendation Letter

Adding to @Kostia's answer, a negative letter from the undergraduate thesis advisor will tank your application.

He is giving all the signs of not being able to write a positive letter. He disagreed when you first asked him, then he agreed to only writing a few, now he is avoiding you.

I would absolutely not use him for any letters if at all possible. Again, a bad letter from your advisor is worse than a missing letter. Try to find a third person and have them write to as many schools as will let you change the letter writers.

A strong letter from the undergraduate thesis adviser would be very valuable, since this is the person who presumably knows your academic achievements better than others. Assuming that your adviser has agreed to write a recommendation letter (otherwise you should not have listed him as your referee), I would recommend to try your best and find him by going directly to his office, or through his colleagues or admin people.