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.