I believe so. The "Getting Started" document encourages such aproximations, you might want to read the chapter "Overall scheme/methodology for running EnergyPlus" in the same PDF.
To: EnergyPlus_Support@ yahoogroups. com
From: m_neves32@yahoo. com
Date: Mon, 1 Mar 2010 20:09:16 +0000
Subject: [EnergyPlus_ Support] 1.Zone = n.Smaller Zones
Does anyone know if itÂ´s possible to have a thermal zone made up from different volumes in a building that my not physically be connected.
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