Turns out as long as your have properly defined everything as per floor area, it propagates to EnergyPlus, so you can just use an EnergyPlus measure to overwrite the zone area.

Here's an example of a Lights object:

Lights,
  189.1-2009 - Office - ClosedOffice - CZ1-3 Lights, !- Name
  90.1-2007 - Office - ClosedOffice,      !- Zone or ZoneList Name
  Office Bldg Light,                      !- Schedule Name
  Watts/Area,                             !- Design Level Calculation Method
  ,                                       !- Lighting Level {W}
  11.8403014583807,                       !- Watts per Zone Floor Area {W/m2}
  ,                                       !- Watts per Person {W/person}
  ,                                       !- Return Air Fraction
  0.7,                                    !- Fraction Radiant
  0.2;                                    !- Fraction Visible

I've uploaded I'll upload a measure to the BCL called Overwrite Zone Floor Areashortly.

Turns out as long as your have properly defined everything as per floor area, it propagates to EnergyPlus, so you can just use an EnergyPlus measure to overwrite the zone area.

Lights,
  189.1-2009 - Office - ClosedOffice - CZ1-3 Lights, !- Name
  90.1-2007 - Office - ClosedOffice,      !- Zone or ZoneList Name
  Office Bldg Light,                      !- Schedule Name
  Watts/Area,                             !- Design Level Calculation Method
  ,                                       !- Lighting Level {W}
  11.8403014583807,                       !- Watts per Zone Floor Area {W/m2}
  ,                                       !- Watts per Person {W/person}
  ,                                       !- Return Air Fraction
  0.7,                                    !- Fraction Radiant
  0.2;                                    !- Fraction Visible