Did you solve this? It sounds like the tool is using the IDs as a primary key and dropping the name label.
We can’t see what is inside of your artifacts, but this tool will let you inspect them. (this suggestion is from a Qiime2 author)
I wonder if you can set up the artifact metadata differently to label your artifact in a way that will preserve the information you are most interested in. The Qiime2 community might be best for this. The tools in Galaxy will work about the same as when used directly since the artifacts ignore the other kind of metadata that Galaxy usually applies to data (all the datatypes are qza or qzv).
This is the forum and it is active → User Support - QIIME 2 Forum. The won’t be interested in the Galaxy screenshots, but they will probably appreciate the views from https://view.qiime2.org. It seems like your idea to map the IDs to the name is where to start but I don’t personally know of the correct tool to use, and I’m guessing other moderators didn’t either since there wasn’t a reply here yet .. that’s why I’m suggesting to go to the experts who use this tool suite the most. Any Qiime2 tools they suggest should be in Galaxy. If they suggest other methods, there might be a way to do that in Galaxy too, it depends, and you can ask.
If you want to post back what worked, that will help others later! And if you solved this already, let us know. 