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EnergyPlus now uses an algorithm that detects if each zone volume is fully enclosed (think leak proof). The algorithm checks to see if each edge of each surface is used touched by just one other edge of another surface. If this does not occur the warning message that you saw will be shown. I would look at that surface and that edge in particular and check if touches another surface edge. It might make sense to visualize the model in Sketchup using Euclid or OpenStudio. It is very likely that the warning message does show a problem with the zone not being fully enclosed. If that is intentional, you can ignore the warning. If the zone is fully enclosed but the way the edges are arranged is complicated you should also feel free to ignore the warning.