yes Inversion is a best option.
Do not invert redirection.
You need to analyse what is wrong and then decide the course of action, otherwise you can create more mess.
- How old are each of your domains?
- How long did you own each of them?
- How long was 301domain.net ranking before you implemented redirect?
- Why did you redirect? Are you moving domains or some other reason?
- If some other reason, why? And how closely is the content related? Are you redirecting page to page or everything to a home page?
- Have you ever had the redirect other way around?
- Also - the manual action is because of content not being good enough. If your maindomain.net got this penalty, but not your 301domain.net, then I presume the content is quite different. Can you put 301domain.net content on your maindomain.net or improve the maindomain.net content?