Hi Justine,
Thank you for the follow-up! Actually, I think your solution here would work perfect for what I'm trying to do, as effectively all I wanted to do was to recalculate the PCoA just without certain samples:
filter a distance matrix (
qiime diversity filter-distance-matrix), recalculate the PCoA (qiime diversity pcoa), and do the emperor plot (qiime emperor plot)
...I just didn't realize this was possible 
. Thanks so much.
(Apologies, I also just saw that you posted a similar response to a sort of related issue here that I somehow missed in my earlier searching on this topic!)