I have a flyback transformer. It has 2 outputs. I'm going to use one of them on a flyback converter.
Should I leave the second output of the transformer unconnected or connect a load to it?
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Well, that depends on what the second output is for. There aren't two equal transformer in the world.
Often the second winding is for auxiliary bias but it could be a reset winding or a second output. Unless you know how it's wound you can't say for sure.
In doubt keep it open