I don’t think that is a mistake. payu sweep just removes ephemeral work directories. The updates to the manifests should remain, though they are not committed to the git repo without doing that manually, or when you next do payu run.
Good to hear it is running and producing some encouraging outputs.
If you need assistance with your configuration, or want to share it more widely, then I’d encourage you to put it on GitHub.
There are some instructions on how to do this in the training material from last year but @helen is working on some updated and more concise instructions that hopefully will be available soon.
I’ll close this topic, but please do create a new one if you need more assistance with this configuration.