I think you mean the Apply to Font button, right? Well, it does the following:
Once you set up one effect (let's say your power up), you set your colour and your blade behaviour (flicker, instable flicker, whatever). Then you apply your sounds to the effect. Once you write it, it's on your saber. I see that's clear to you.
Now, if you decide to change the blade behaviour or colour or whatever, instead of setting up the font from scratch, you can just do the changes and then click "Apply to Font" which saves the changes to the saber, but it doesn't upload the whole font again.
I don't have a Diamond myself and thus I haven't done that yet, but from what I read and heard about Diamond, I'm pretty sure this is what "Apply to Font" does.
This sums it up nicely but it is Write to Board.
I have two Diamond Controller sabers.