Hi Spencer,
I don't know if this was ever resolved for you, but I've been converting biom tables back and forth for different analyses lately, and there are a couple of things to remember.
Use convert_biom.py --help to see the current syntax for your command
To convert from biom to txt (tab delimited), use the following:
convert_biom.py -i otu_table.biom -o otu_table.txt -b
However, this command leaves the taxonomy behind, so upon conversion back to biom, you will be missing some crucial metadata. Write the taxonomy into your tab-delimited file this way:
convert_biom.py -i otu_table.biom -o otu_table.txt -b --header_key='taxonomy"
When converting back to biom, you must specify table type, and your metadata (taxonomy) field:
convert_biom.py -i otu_table.txt -o new_otu_table.biom --biom_table_type="otu table" --process_obs_metadata="taxonomy"
Hope this is helpful