This is why staggered hatches can be problematic, unless you have a separate hatcher. Next time, you might be better served by planning your hatch so that the chicks and ducks hatch at the same time-- set the duck eggs a week before the chicken eggs.
At this point, absent a separate hatcher, you have two choices:
1. Don't turn the duck eggs for the duration of the chick hatch, and hope it doesn't hurt them; or
2. Reach in to turn the duck eggs, and do it quickly, hoping that the loss of heat and humidity doesn't hurt the hatching chicks. Don't know what your set up is, but you might try sticking something through a vent hole to turn them, or just hope the chicks kicking around in there do some turning on their own.
Which eggs are more important to you-- the chick or the duck? If it were me, I'd probably leave the bator closed for the duration of the hatch, and take my chances on not turning the duck eggs. The ducks are fairly well developed by week 3, and less likely to stick to the shells. Prevailing wisdom of this board seems to be that regular turning is most important during the first couple weeks of incubation.