The idea of Homeoprophylaxis is this: if you take a remedy while you are still healthy, the remedy may not create physical symptoms, but it will still affect your body energetically. In other words, the effect of the remedy will be in your energy field, and it will also stimulate an immune response from the system.
So, what happens when you encounter a disease with similar symptoms? Since you already have a similar energy pattern in your system created by the homeopathic remedy, this energy is most likely stronger than the energy of the disease itself; therefore, the stronger (homeopathic) "disease" knocks out the weaker (the true disease), and you don't get sick because it never reaches the physical (in other words, you are no longer susceptible).
It doesn't matter which of the two reaches your body first, whether you are sick and take a homeopathic remedy, or whether you take a homeopathic remedy and then encounter the disease. It works either way, because it is based on the same homeopathic principle, that you can't have two similar "diseases" in the body at the same time, and, as I said, this observation is based on natural law--the way things always happen in nature. (Another natural law is Hering's Law of the Direction of Cure: from the top down, from the inside out, from the most vital organs to the least vital organs and in reverse order of occurrence).
This principle also explains why, in some cases, people still get sick, even though they may have taken a remedy as a prophylaxis. If the remedy they took was weaker than the disease they encountered, the disease will make them sick and knock out the effect of the remedy instead. Therefore, it is important, when taking a remedy prophylactically, to make sure to try to match the potency to the intensity of the disease.
Whenever your understanding about something is based in natural law, it isn't difficult to come up with scientific proof if anyone should need it. But, since we already know that anything based on natural law works, providing scientific proof is of very little importance in my opinion because if something works, it will work regardless of how many scientists you are able to convince of it intellectually.
Unfortunately, "science" speaks a different language than homeopathy because it is not based on natural law, it is based on theories and conclusions, and the conclusions, then, become "the accepted truth" only until someone else comes up with a better "truth." This is why science keeps changing concepts over time. If science were based on the understanding of natural laws, a lot of wasted effort and money could be completely eliminated. Knowing this, I find it strange that a science, which is actually based on natural law, like homeopathy, should have to prove its findings to a science that has no understanding of how these laws work. This simply doesn't make a whole lot of sense to me.
Galileo told the courts that he was willing to withdraw his statement that the earth was round, but he warned that withdrawing his statement wasn't going to change anything. It is time for things to change...