When I did a batch of 30 I had 25 energy of the effect and it consumed 5 energy of PowerCode. Doing a batch of 45 consumed the rest of the effect. I think there are two possibilities:
1. The total of items crafted in the batch must not exceed the active energy of the effect or it will start to be burned.
2. The effect is consumed whenever you exceed 25 items in a batch.
I'll take a look at it at rollover to see if this is the case.
Edit:
Doing a batch of 50 with 50 energy of PowerCode did not remove any energy of the effect so it looks like you don't lose the effect provided the batch isn't too large.
Gone fishin', be back at dark-thirty!