Honestly (I am going to get chewed out for this :/)
The worst I have read about a D3 overdose is that if constant over-supplementation is occurring over a long period of time it can lead to kidney problems, ulcers, and gout.
Babies need D3 to utilize their calcium properly. If it were me, I would leave a dish of vionate (or calcium, Vit A, Vit D3 mixed) in with the gecko to lick as it needs. So assuming it knows what it needs (highly debated) if you actually did overdose the D3, it might wait a few days before licking it and self regulate on its own.
Another option: use a UVB 2.0 bulb for a few hours a day. It is hard for them to overdose on D3 when it is produced naturally with light. If you do this, the baby needs to have a hide that has enough room for the baby to be in the complete dark and avoid the light if it needs to.
That said! Many other members will have a lot to say about this. Since you have chosen to dust and are following their schedule, they are the experts on how much you need and how to correct problems with their method. I can't help you there.