Letters of Recommendation when applying afresh to a new PhD program
(Again, for the U.S., especially in mathematics, my field...) Generally, the more recent the basis for letters, the better, by far. For that matter, having 2/3 of your letters be pre-graduate program might make admissions committees wonder what happened in your graduate work.

If you can get an absolutely stellar letter from undergrad, that might be helpful, but also really try to find two solid letters from your graduate program, attesting to your capacity for graduate work, rather than just saying you aced undergrad material.