It should be equivalent or better. Moby 2 is a stronger AI engine than Moby 1, so analysis quality typically improves. The format will look different — Automations default to a clean HTML report instead of the plain-text output Agents produced.
If you paste an Agent prompt into the migration flow and the kickoff output looks wrong, tell Moby in the same chat — it updates the Automation in place. For prompt-level drift, see My Automation is giving different output than my Agent was in the troubleshooting hub.