I'm presently in a master's program. The program is much more relevant to the area I wish to do a PhD in (I switched majors from Bachelor's->Master's). I took two recommendation letters from my undergraduate institution to apply for master's, but the strong one was about a relatively unrelated subfield and I have not kept touch with the professor in question due to the switch. I'll be applying 3 years post undergrad. In this situation, can I forego the folklore rule of 1 letter of recommendation from an undergrad university ?
I don't see much value in a letter from an old relationship that is no longer relevant. Your recent work will almost certainly be considered more heavily than anything you did as an undergraduate. (Extraordinary cases aside.)
Get letters from those who know your work and can make a (positive) prediction about your likelihood of success in the new program. That probably means professors and/or advisors from your MS program.