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Currently The Hobbit films are rumored to start filming in February for a year plus long principle photography schedule. However, Bleeding Cool is reporting that Sherlock will begin its filming in May. So what to do?
Well it seems that The Hobbit script itself helped provide a solution. The film will have many scenes that will more or less be Baggins-less including an attack on the White Council and others. As a result the plan seems to be to have Freeman prep (costume, makeup testing, etc) and film starting in January to May, head to the UK to film Sherlock for however long that will take (probably a month or two) and then return to The Hobbit. During that break Jackson will simply begin filming the scenes that do not require the actor. In most circumstances this would probably be unheard of but then again most books don't have a lead character that spends a great deal of time being invisible.