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You are correct that the "Zone Windows" output is the sum for all "Surface Window" outputs for a given zone. One caveat is that these are both reported "... when that sum is positive" for zone windows and "... when the total heat flow is positive" for individual surface windows ie. when heat is flowing from the exterior to the zone. You may need to also report Surface Window Heat Loss Energy as an output to see when window surfaces have heat flowing from the zone to the exterior. For a given timestep, the sum of all "Surface Window Heat Gain Energy" MINUS "Surface Window Heat Loss Energy" outputs should equal the "Zone Windows Total Heat Gain Energy". Likewise, the sum of all "Surface Window Heat Loss Energy" MINUS "Surface Window Heat Gain Energy" outputs should equal the "Zone Windows Total Heat Loss Energy" output.
Another output to consider is Surface Window Net Heat Transfer Energy, which accounts for radiation from the opaque frame and divider components.
You can read more discussion about window surface outputs on this UnmetHours post.