Ok so I looked through YS and found a couple of instances where they talk about rearanging your character (trading stunts for powers too).
This one:
Musts: Pure mortals may not take any supernatural
powers. In exchange for this restriction, pure mortal characters get a +2 bonus to their starting refresh. If this character ever takes a supernatural power, this refresh bonus goes away immediately (which may be mitigated by dropping one or two mortal stunts).
I bolded the section I am talking about. This is kind of iffy though. It could be seen as a special instance since the Pure Mortal is losing two refresh.
This one though:
Completely Revising Characters
If there’s enough downtime in your story between a major milestone and the next adventure, you might also consider re-creating your characters as a group— adjusting aspects, reconfiguring skills, buying stunts and powers, etc. While you don’t need to go through the phases part of character creation again, it’s a chance to rethink or replace your character’s high concept.
As long as there’s some commonality to the character for a sense of continuity, this isn’t a problem.
This one seems to be more what we are looking for. I bolded the part I think is most important, but it does seem like you should be able to recreate your characters refresh spent durring a milestone, but it does say a major milestone so yea.