Thanks Matt. I figured that the it was something like that holding it up. I went ahead and added back those missing 17 samples and gave them dummy values and saved that file as "metadata.txt" but after I ran the emperor plot command again, I got an error saying that the file did not exist even though it clearly does exist in the same directory as the rest of the data files:
(qiime2-2017.8) Helps-MacBook-Pro:~ lisacrummett$ qiime emperor plot \
--i-pcoa core-metrics-result/unweighted_unifrac_pcoa_results.qza
--m-metadata-file metadata.txt
--p-custom-axis Exper.Day
--o-visualization core-metrics-result/unweighted-unifrac-emperor.qzv
Usage: qiime emperor plot [OPTIONS]
Error: Invalid value for "--m-metadata-file": Path "metadata.txt" does not exist