I've done this, and it works. Just make sure you gather up everything you want from your houses, or you'll lose it. You'll also lose any new HF items you're carrying. My biggest loss was all my salmon roe that took hours to collect. Oh, and Nostor's Helmet which I forgot on a shelf in one of my houses.

http://www.uesp.net/wiki/Skyrim:Hearthfire_Items