Hi @pbrannock,
From where did you download the silva-138_2_ssu_nr99 files? Assuming these are QZA files, what version of QIIME 2 was used to make them? You can view that in the provenance with QIIME 2 View.
Without looking through the files, I'd guess that this error is related to any prior editing / parsing of the taxonomy file. It is okay for the taxonomy file IDs to be a super set of the sequence file. It appears this error is the other way around, where the sequence file IDs are a superset of the taxonomy file.
To be safe, I'd recommend using qiime rescript edit-taxonomy ... to make any taxonomy adjustments. This will minimize unexpected errors.
Also, I'd advise against using --p-mode 'super', with SILVA taxonomy strings. As this can result in hybrid non-sensical taxonomies for some groups. I'd leave this parameter set as --p-mode 'unique'.
Finally, that version of QIIME 2 is almost 2 years old. I'd inquire about installing the most recent version (2026.1) on that system.