You can make it work, but you might get a slightly lower hatch rate than if you had incubated your two lots of eggs separately.
When you put the first set of eggs into lockdown, you'll still need to turn the second set, so you won't be able to run a proper lockdown, as you'll still need to open the bator to do this, unless you have an auto turner and can figure out a way to have some of the eggs in the turner and some of them out of it. You'll also need to bump your humidity way up, and when I'm doing this, I like to have it higher than I normally would in lockdown, to compensate for the bator having to be opened 3 times a day. If your humidity has been good up till then and your eggs have lost the correct amount of moisture, a high lockdown humidity is perfectly safe for them.
Then, once the first lot of eggs have hatched, drop your humidity for the second lot of eggs down to much lower than normal for a few days, to compensate for the the high humidity that they were subjected to. That way, they should reach their lockdown with the correct moisture loss. If you weigh your eggs to gauge moisture loss this is dead easy, if not then you really just have to look at teh size of the aircells and do a bit of guesswork...
I've done a couple of staggered hatches like this, and I usually get a typical hatch rate for the first lot of eggs, and a lower than normal hatch rate for the second lot, probably because the fluctuations in humidity aren't ideal, and also because of the hatching debris and resultant bacteria buildup in the incubator after the first lot has hatched.
Good luck!