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From what I understand, Google sees section.mysite.com as a seperate site from www.mysite.com. So my question is, how will the sandbox affect this "new" site, taking into consideration that it has identical content to the old, and all of the old pages have been individually 301-redirected to the new?
Will I likely have a few-month waiting period before I can get any decent rankings out of this, or should it be rather instantaneous (a few days/weeks)?
My best guess is that the time to seeing the subdomain all back to normal will depend on natural inbound links from other domains. If they are healthy, then the 301's should carry through in a few weeks. If the only inbounds (or almost all) are on your domain I wouldn't be surprised to see a slower process.
And if you can get some natural inbonds to change the link to the new url form, that would be excellent. You might also do well to implement the base href tag on the new subdomain. That can't hurt and might help.
I'd be very interested in hearing how this works out for you. It's been many months since I set up a subdomain anywhere, and I've been steering clients aways from the idea unless it is a necessary part of a solid, long-term business strategy.
I am pretty sure you will have a bump in the road -- the question is just "how big?"