If there are several incidences/prevalences for a pathogen at the same time and location, pick the estimate that we are happiest with or combine estimates somehow.
Identify estimates where we need choose between estimates.
Add a flag for such estimates.
Create tests, that require us to specify our preferred estimate, for cases where there are multiple prevalences/incidences for the same pathogen, time, and location.
If there are several incidences/prevalences for a pathogen at the same time and location, pick the estimate that we are happiest with or combine estimates somehow.