Hi @hughesd
Yes, that older post is still valid. An “undo” function is still pending. There are a few topics about that here, too, that I had forgot about yesterday, but this is probably the best one → Remove installed databases - #2 by jennaj. Notice how that was for a specific tool – and that it involved a few tables. Maybe good to know for later. In short, trace back through what the original DM touched and pick out your changes. Then restart the server.
For the DM you are using, there is less data to tidy up. It would be those two tables plus any associated genome indexes themselves such as the fasta + fasta.fai (although the data files would be ignored if the tables do not reference it, and you are not tool concerned about the storage space).
Glad you are working this out! Maybe someone will see this and take on a project for the undo tasks. The reason why this isn’t higher in priority is mostly that the administrators are using Ephemeris to load up genomes onto instances in a batch, or in response to tool installs. That is all done through PRs with built in checks on the public sites.
- Welcome to the Ephemeris documentation! — Ephemeris 0.10.11.dev0 documentation
- Then included in here (and in other admin resources at times) → Hands-on: Reference Data with Data Managers / Reference Data with Data Managers / Galaxy Server administration
The undo would probably fit best into that application, for maybe the gxyadmin utility. If you know of anyone looking for a project, or anyone else reading this who is interested, this would be a good discrete project with a clear end goal and grateful users! Maybe for a grad student or someone looking to build up open source projects for their portfolio. They would get support from our team! I’m pitching now! 
