...In MOST cases a bad egg won't affect the good eggs, but it does occasionally. It's very important that no flies (especially the small gnat-like ones seen in the warmer months or warm climates) have no access to the clutch. Maggots can overwelm the clutch. Barring this the bad egg's contents will coagulate and dessicate and microflora (bacteria and fungi) common to eggs will not spread to good eggs because of immunity factors of the good eggs.
...this being said, if the bad egg is not adherent to a good egg, remove it. If it IS adherent to any great degree, removal can be nearly impossible without damaging the good egg(s). Removal is easier in the first few days post-laying; after this period it is best not to try unless you have a good set of probes and a lot of patience. A good mother will return to her eggs no-questions-asked, but the occasional female won't. Females will leave the clutch normally anyways to thermoregulate or to drink, so separating her from the clutch for upwards of an hour or so rarely will do any harm. Again, a good mother will rapidly return to her clutch. After this do not disturb her.
Good luck!
Scott J. Michaels DVM