There is an option in Slic3r to disable cooling for layers that take more than n seconds.
What would be the disadvantages of having cooling on big layers ?
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Warping. Especially with materials like ABS, you want the plastic to cool down as gradually (and slowly) as possible, to prevent the print from warping as the cooling plastic contracts. On small layers, cooling is usually mandatory: with really small layers, you just end up with a big glob of molten plastic if the previous layer hasn't solidified enough before the next layer is put on top.
You want just enough cooling that the plastic holds its shape, but no more than that. On a large layer, the plastic cools enough naturally without help from a fan.