Outdated letters of recommendation for graduate fellowships
It is perfectly normal to have one letter from your current research, since you presumably only have direct, extended experience with only one faculty member.

In picking your letters of recommendation for fellowships, the most important criterion is who can comment meaningfully on your potential to become a researcher. Whoever can provide the strongest letters should be your top priority. 

However, I would tend to lean against asking someone who has never written for you before to do so after a gap of some years without providing more recent information on what you've been working on since.