You can try if you want... but trying too close to medicating increases the chance of birth defects and decreases fertility. Reason being is the the drugs often act as an competitive inhibitor of some other biologically necessary component, or stops some required functioning of the organism, thus preventing the reproduction or causing death to the living things with faster life cycles within the chicken. The reason the drugs don't kill the larger organism or animal is that because their life cycle is longer, the "short" interruption to biological processes is tolerated. However, during the development of an embryo, the cells are dividing faster and a single mistake in growth can have huge results. One mutated cell on your arm as an adult won't kill you and you will still have an arm. One mutated cell on your future arm to be when you are only 100 cells total, will leave you either dead or without a part of your arm.
For example, someone undergoing cancer treatment loses all their hair and end up with terrible stomach pains and intestinal complications due to chemo. The body as a whole lives though the process, ideally without the cancer. The common link between the cancer tissue and tissues such as hair and intestinal lining is a fast cell cycle, meaning they divide quickly. If you give a drug or treatment to kill fast growing cells, all fast growing cells will die. Similarly, the growing embryo is growing and dividing as fast as the worms or parasites you are trying to kill, thus potentially kiling or damaging the embryo.
So in short, best toss the eggs if you want to hatch healthy chicks, or you can try to hatch them, but be ready to cull chicks with deformities and accept a potential low hatch rate.
As for your medication of the birds in the first place, if you didn't confirm a case of suspected parasites, it is possible that the drug will not work in the future and that runny poo could be an issue of weather and drinking more liquid to keep cool.
