FRANCIS UPDATE

Lindesfarne, I really wouldn't worry. A very small number of Danielle's eggs could have been incompletely transformed. Remember when Martha came back through the portal but remained human? She went through in a lead-lined barrel. I hypothesize that if there was enough lead in her blood, maybe not even enough to cause symptoms of lead poisoning, it could have blocked some of the transformation of her cells. And the changes could have only partially affected a couple of eggs in only one of her ovaries. Only testing a couple of eggs might not reveal any human DNA.
I believe my slight blood lead levels theory could work, because as an auditor she could have had to go on-location to places that weren't paying their taxes. If they're not paying tax, then I doubt they're following the health codes, and may have peeling lead-based paint, lead dust in the air, etc.

I don't think you really need to worry about your children if that's the case. You went through the portal as a baby, so I doubt you had enough lead exposure to cause any issues. And Danielle had only been on your side of the portal for a short while when she became pregnant. We aren't sure exactly how the portal works, and maybe some cells take longer to change their DNA. Maybe some internal cells are transformed by residual effects. Maybe mass affects the portal's effectiveness. If it uses beta radiation, it might have trouble going through a certain thickness of tissue. Again, you went through as a baby, and with the low mass babies tend to have compared to adults, I doubt that that would affect you, while it may have affected Danielle's trip. You were accidentally tossed through the portal, but Danielle was forcefully thrown through. Danielle could have been shot through at a far greater velocity, meaning the portal would have less time to act upon her, and so it could have missed a couple cells, including some of (but not all of) her eggs. Conversely, you were unintentionally sent through the portal, undoubtedly at a lower velocity. Less mass, fewer cells, and more time for the portal to act upon you could translate to a more complete DNA transformation.
Plus, I have read that the immune system tends to try to eradicate "foreign" DNA. This is part of how it fights viral DNA strains. Once the majority of your immune system was transformed, it would do cleanup of any untransformed cells. This would likely take time, perhaps several years, leading to an untransformed egg becoming fertilized with Fennec Fox DNA. However, it's been so long since you've gone through the portal, I bet the "cleanup" is done, and if not, it certainly will be by the time you and Fenton are married.

So, Lindesfarne, a scientist like you can certainly recognize that there are far too many variables that could contribute to Francis' genetic diversity. I'd wager the odds of your offspring possessing any human DNA to be negligible. So don't worry, enjoy your life, continue studying Francis, because I know you're interested in how his DNA is so unique, and you may find things to help Francis along with life, like vaccines his body may be more receptive to. Observing his behavior as well may give you useful information too. Continue your research for Francis' good, and for Danielle's comfort. But you don't need to worry. Francis is healthy and happy, and you're so observant and intelligent that you may end up giving Francis a GREAT advantage in life. Don't worry about your children either. Even if they do retain some human DNA (which I greatly doubt they will), so what? Humans have their advantageous traits. And interspecies offspring in your world have no issues, why should human/hedgehog/bat offspring be unhealthy?
Also, about Francis' teeth: Wait until his adult teeth come in. Humans have two sets of teeth, the first set tends to come out between ages 8 and 15, and the second set comes in during that time. His baby teeth may be humanoid, but his adult teeth may still be canine or rabbit-like, or a combination of the two.

Again, even though this is totally redundant because I've stated it at least three times in this post, and many other times in previous comments, but I seriously believe there is no reason for you to worry. Que cera, cera! Hakuna Matata!

/me plays the Twilight Zone theme just for erm.