In the past five years not one of the communities we’ve worked with has seen any SEO hit as a result of the above. Google has publicly stated that subfolder vs subdomain has no impact on SEO, something that Jeff has also reached out and had confirmed directly.
You’re wasting your time creating complexity here rather than identifying and fixing the real issue, and as it has been more than a month Google won’t magically “turn the faucet back on”.
Proxying Discourse through DNN and IIS is going to murder your TTFB, which will have more of a negative SEO impact on top of whatever you did back in September/October.