Well there are 4 different forms of Paratyphoid:
1. Bowel form - weight loss, lethargy, green diarrhea, loss of appetite, rapid death. Usually seen in very young youngsters with no natural immunity
2. Meningeal form - Effects the brain, causing it to twist and hold its head in unusual positions or become paralysed
3. Joint form - Swollen, red, painful joints of wings and legs
4. Generalized form - Multi-organ involvement, ususally seen as a very sick bird, rapid weight loss, short clinical course leading to death. Bacteria sometimes localizes in gonads (which both hens and cocks have), causing infertility in both sexes. Hens that continue to lay often produce infected eggs that fail to hatch or infect the young that hatch.
Sounds like it could be either 1 or 4. 4 would make sense, since it deals mostly with the eggs. But the bowel form would make sense with the babies that do hatch. The parents could be immune but still carry the disease through contaminated food/water, and pass it to the children.
Anyways, like I said, it could be just about anything, or nothing at all other than bad luck. Some medicine is a good idea just in case
Use the Baytril. It's good for respiratory problems, as well as for the unknown cases and for salmonella (includes paratyphoid and e coli). It'll be your best bet if Paratyphoid IS the problem. Tetracycline could be used as well but I think Baytril is better. It's pretty broad-spectrum.
It does kill the good bacteria too, so probiotics afterwards is important. If you don't have anything, you can just use a tablespoon of apple cider vinegar per gallon to raise the acidity in the bowels and promote the growth of good bacteria. You can put ACV in the water everyday if you want to keep them healthy, or you can use it less often, it's up to you.
Also, don't let them sit on any eggs until about a week after their Baytril course (you can use dummy eggs so they aren't so stressed from taking their eggs). Baytril can be pretty harsh on the system and can cause some problems if the hen lays eggs while still being treated.