My fiancee has had quite the battle with this pilondial beast. He had an extremely active cyst flaring up almost every four months over three years, until he had excision surgery twice. Excision may or may not work depending on if the surgeons remove all of the cyst. If there is ANY bit of the cyst or tunnels left, the cyst can regrow. Hence my fiancee's two surgeries! So far the second has been successful *crosses fingers*. At our consultation with the surgeon, he explained that they really don't know much about these cyst and why the happen. He also said that flare-up's can occur quite at random. Some people have one flare-up and then a second flare-up thirty years later. Other people like my fiancee have frequent flare-up's. Having the cyst excised is a matter of personal choice. Your husband has to decide whether the pain he has during flare-up's is enough to warrant surgery.
Also, how long it takes for flare-up's to clear up is quite variable. I have a feeling it depends on the size. My fiancee had some small infections that clear up in less than a week. He had another flare-up that literally looked like a golf ball was under his skin. It kept growing and wouldn't drain, so I took him to emerge to have it lanced. In lancing they slice open the cyst, clear out the infection, and the remaining hole is packed with gauze for weeks until it heals from the inside out.
So if your husband's cyst is draining on its own, that's a good thing, it means the body is trying to clear the infection out. From my fiancee's experience, I recommend sitz baths and keeping the area as clean as possible.
If the infection has cleared up by now, it now becomes a waiting game and your husband has some decisions to make based upon the frequency of his flare-up's and his level of discomfort during them.
I hope this helps! If you have any other questions I'd be glad to help.