Thanks for following up and reporting. It appears that this is an issue related to setuptools (this is a deprecated package that has been fully removed in our current development cycle). This isn't something I've seen before, but let's see if a re-install fixes the issue. Try running the following:
conda install --force-reinstall setuptools
This should hopefully resolve these annoying messages, but I'd test out a few commands after completing this just to confirm.
Apologies for the delayed reply, I missed one of the earlier notification emails in the thread, sorry for that!
I was able to solve the issue following what you said: by setting channel_priority to flexible and downgrading conda to 25.11.1.
Truly, a huge thank-you to you and to the entire QIIME community here. I’ve been using QIIME since the QIIME 1 days, and the support on this forum has always been incredible. Not only do I always get help, but I also learn a lot from the answers given those of many other users. Great people.