Flow box removal?

Hi,

Just a quick querie from a rookie: Winter has set in and I just checked my hive through the windows. The colony was doing well but the top box with flow frames is now completely empty of bees. I left it on as our winters are relatively mild (melbourne) and there is honey in most frames. Will the bees be ok with the empty box on top? Will they go back up when we have better weather? (Rain and coldsnap at the moment) If I leave it on will the honey crystallise?
Thanks for any advice, much appreciated.
Paul