The actor who played him, in the intervening years, turned onto kind of an asshole, Twitter troll, hardcore Trump supporter with all that implies, etc. He and Lynch don't get along anymore, and I'm sure there was some fear of him saying things that would make everyone embarrassed by his presence on the show.

EDIT: Here's an article.
http://mashable.com/2017/05/22/twin-peaks-michael-j-anderson-david-lynch-man-from-another-place/

Conveniently, the last thing The Man From Another Place says in the original show was "When you see me again, it won't be me."