How to remove unwanted aftertaste from food
There is probably no universal means.  Don't store strongly flavored liquids in plastic bottles you would like to reuse.

In the specific case of hot chocolate, it is ammenable to a number of strong flavors which may mask the odd orangey aftertaste.  I would recommend re-heating it with a pinch of cayenne pepper (really; hot pepper and chocolate go nicely), and perhaps a couple of cardamom pods if you enjoy their unique flavor.