Thanks for the suggestion! I was thinking of doing what you suggest: exporting the FeatureData[Taxonomy] artifact and just grepping for the taxonomic classifications that I had filtered (no hits if they were indeed filtered. However, do do this I need to first filter the FeatureData[Taxonomy] artifact to match the filtered FeatureData[Frequency] artifact. Otherwise, grepping the exported taxonomy table will generate hits for “mitochondria” or whatever taxa that I wanted to filter.
I could export the taxa-filtered FeatureData[Frequency] to a biom, then convert to .tsv, then find the intersection between that .tsv and the taxonomy.tsv. However, this is a lot of steps just to check that taxonomic groups have been removed.
As far as I know, there’s currently no way of filtering the FeatureData[Taxonomy] artifact in qiime2.