A little more tinkering and I figured out that I actually don't need to merge BLAST & naive-Bayes taxonomies for my work, so not an urgent issue.
I will provide what info I can for figuring out the bug in case it's something you want to look into more. Unfortunately, I don't know how to trim the taxonomies themselves and don't have the capability to recreate them on a smaller dataset at present.
I'm currently running QIIME2 v2021.4.0 and RESCRIPt v2021.8.0.dev0+3.g1ce2142
The taxonomies I was attempting to merge, and the naive-Bayes classifiers used to create them, were created on QIIME2 v2021.2 and unknown RECSRIPt version installed April 2021. Some computer issues meant I had to reinstall QIIME2 recently.
The taxonomies I was merging aren't all that large, so I'm going to upload them here in case you want to play around with them, along with the script I ran to get the errors (exactly as above, but including loading the QIIME2 environment, etc).
Finally, I ran into another issue with merging taxonomies that I will post separately soon that seemed like it could be related. I will link it here when it is posted. Maybe both issues are just from using QIIME2 v2021.2 artifacts in newer versions of RECRIPt and QIIME2.