Hi @Kat,
It sounds like your merging protocol is disrupting the format expected by biom. I do not really know the answer to this specific error, since biom support questions are not covered by this forum (biom format support is on the qiime1 forum) but I may be able to offer an alternative.
See this post. Specifically, using the biom add-metadata command should do the taxonomy merging without the need to convert to tsv and round-trip back to biom format. In general, biom format files are much happier when the biom commands are used to modify files.
That would give you a biom with taxonomy merged.
I hope that helps!