I would do 2 vaccinations then. Wait for everyone in batch 1 to hatch, vaccinate and discard remaining vaccine. Then, using a fresh vaccine bottle, vaccinate batch 2 the following week when they are done hatching. Vaccinate as soon as you can once everyone in the batch is hatched.
Again I think...
I would wait for everyone to hatch and then do it then.
How staggered are the hatches? I think 24 hrs of age is not extremely strict.... You can vaccinate on day 2 or 3 as long as they haven't been exposed to outdoors. This includes dirty hands/clothes.