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RewriteCond can be used to check the requested subdomain in the HTTP_HOST variable, and execute the rule based on that being "wiki". I don't advise it.
I suppose that would be a good strategy?
I don't understand what you mean by "301 the whole folder to the top level domain". You need to think about both "URLs the user sees" out on the web, and "internal paths to real files" inside the server.
They are two different things that are only 'associated' but NOT equivalent.
If you change URLs you need to redirect old URLs to new URLs.
You also need to rewrite URL requests to internal server file paths, adjusting to suit.