Hi @sanda,
I think you’re missing what the taxonomy object represents. The taxonomy is a type of metadata which describes the ASVs (if you did DADA2, you have amplicon sequence variants [ASVs]; if you do clustering like vsearch, you have Operational Taxonomic Units [OTUs]). When you rarify your ASV table, it changes the ASV counts, but not the taxonomic labels. You can also have a taxonomic label for ASVs that aren’t present in the table; in QIIME 2, it doesn’t affect the way these objects relate to eachother. If it’s a problem in R, you can always filter your two dataframe (or equivalent objects) so the labels match. I think thats as simple as setting your row names and then using the indexing stuff, but again, Im not an R person.
All that said, you don’t need taxonomy for ASV-level diversity analyses (and Im a big proponent of ASV-level diversity analyses… there are some discussions here and here as to why.) I would recommend a phylogenetic tree. You should only collapse and rarify (or rarify then collapse) if you have a good reason to collapse your taxonomy.
Best,
Justine