It's referring to a previously mentioned noun, I suppose. It's to avoid being redundant.
Here are the cupcakes. Choose one.
It shouldn't, because "Choose one" doesn't make much sense without there already being something to choose from. In English, it is not necessary to say, "Choose one of them," but in French, it must be stated with en.
I think making the English "Choose one of them" would be better. Technically if you are being asked a multiple choice question and one of the answers was "1" then "Choisis un" could be used.
However I probably learn more by coming to look at the comments and this caused me to come and look at the comments so I can't complain too much. :)
The ironic thing is, I actually had two correct answers to choose in the multiple choice.
why not "choisissez-en une"? it's an imperative whether its tu or vous and can be feminine or masculine article
Certainly. It can be "choisis-en un", "choisis-en une", "choissisez-en un", or "choissisez-en une".