Hot peppers in soup don't stay spicy
The perception of "spicy" is completely dependent on the person. And there is a "tolerance building" thing going on too: what is intolerably hot for somebody not accustomed to heat might not even register for somebody who eats hot frequently. As an anecdote, I had a friend who started eating hot. After a month, she started asking the cook to use pure tabasco instead of tomato sauce on the pizza. After another month, she complained that the pizza was made with tomato sauce and the poor cook had to let her taste her from the bottle to convince her that the pizza was indeed made with pure tabasco, it just didn't have the same "kick" for her after habituation. 

From your description of your soup only feeling hot enough for you after adding six habaneros with the seeds, it seems that you have developed an extremely high heat tolerance. And this would be an explanation for what you observed. 

Six habaneros will contain a certain amount X of capsaicin. When your soup is fresh, the pepper has enough capsaicin concentration that you notice it and enjoy it. 

But when you leave it alone, the broth dissolves the capsaicine (unlike pure water, the fat and maybe also the solvents from the vinegar enable it to do so). So you end up with a kind of "capsaicine tea". 

But remember that you have the same amount X of capsaicine, this time diluted in litres of soup, as opposed to sticking all in one bite of pepper. So, now that you bite on the pepper, you don't get the heat. But when drinking the broth, its concentration is so low that it does not register for somebody with a high heat tolerance. From your subjective point of view, the heat has "disappeared". 

The original intention of the recipe author was certainly that the whole soup becomes somewhat hot. And for people with less heat tolerance, it will work well. They will be able to eat the broth and notice the heat, even with much lower quantities of hot pepper. 

For you, it seems that you still haven't reached the dose which will work for you in a soup. So you can add more capsaicin - either use more peppers, or find a source for hotter ones. If the logistics are a problem, buy them dried. But note that at no point will the whole soup taste as hot as the single fresh pepper (due to the dilution), and also that you will become habituated with time, just like my friend with the tabasco pizza.