"we keep a reference on a UIFont prefab as reference to a UIFont prefab with dynamic font"
Not quite clear on that one.
If you have a reference font pointing to another font prefab that you change at run-time, then everything should work fine. However... there may be an issue related to when you swap the font. If it's between Start() calls for example. You need to make sure that you do the font swap first when loading the scene -- in Awake(), before everything else.
Exactly, that is the pointer as you described how to workout the font change in runtime, but we have a switcher for languages in option menu, so, we have to change language on the fly.
we have same trouble of dynamic fonts, just when open/close (enable/disable gameobject with UIPanel) windows, but that appear only one time in game session.
Confirm. We have the same.
The only fine solution I have found is to update all label in the visible panels, just by changing the text to empty and again to the previous one (kind of hack, I know

).