You can cold crash in the primary, secondary, or bottle. I personally have started to do it in the secondary to get the beer off the trub for conditioning, and then to clear it up before putting it in the bottle.
If you have chill haze in your bottles you can cold crash them and it will clear them up in a week or two, but that material is still in there and can be stirred up pretty easily while pouring. Would rather not have it in the bottle at all.
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