the life expectancy of fuel cell foam varies depending on the manufacturer, a friend just found out the hard way that jaz foam only lasts about a year, i called fuel safe and they said theirs will easily last 5 years. this would suggest that for long term storage you would want to drain the tank and pull all the foam, personally i doubt this would help as the fuel residue will stay on the foam for a long time. fuel safe also told me that biggest threat to their bladders is water, so make sure you keep it high and dry.
race fuels are damaged most by UV rays and air, so if you're concerned about the fuel it is probably best to fill the cell and cap the vent and pickup.
We usually try to pump out the remaining fuel in the cell to keep it empty and to figure out mileage stuff. Not sure if this is the right thing to do but again it is only empty for a few weeks at a time.