Chooks4life - thank you so much for all the information. I was trying to find an answer to a problem we have encountered recently and upon reading all your valuable information, I am hoping we can find out what is going on.
You're welcome, I'm still quite the learner myself though. Everyone will be for life, it seems, it's a very complex subject and more info is being found all the time, and plenty of the old info thrown out.
Greetings and
We have 1 rooster and 6 hens and we save eggs, incubate, hatch, etc. Our production has always been extremely good - probably 97% fertility rate. In Oct, we incubated approximately 38 what we assumed were fertile eggs, but about 50% of them were not fertile. Tonight, we just candled 36 more eggs and this time only 10 were fertile. These are the same 6 hens we have been using for a year and a half and now all of a sudden, it seems our rooster must have a few favorites.
It's pretty normal to have favorites, the older and more experienced they get, the more they tend to become discerning about mates; this goes for both genders. Generally by the time they're two or more years old they are quite solid in their preferences. I've found there are very few hens and roosters that will continue to mate with just any chook for their whole lifetime, and there's good reason those 'low standards' hens and roosters take anything they can get. They're never high quality themselves. (I'm referring to the overall package there, not show quality for example --- more the hidden factors we can't detect that chooks detect about one another, as well as their health, instinct and intelligence levels, and so forth).
Even a low quality chook tries to mate above its quality level but they are naturally very averse to mating below it. It's a genetic directive I guess you could call it, generally only quite low-instinct chooks flout that rule, and very young adults often (but not always) fall into that category, so will generally mate all over the place with little regard for the quality of the mates they choose.
Absolute refusal to mate can also indicate a very bad match. Of course, there may be many more things at play here though. Have you watched them and seen whether he associates with all of them at least once a day, or whether some hens avoid him? Is he at all aggressive to them? Is he rough when mating?
Some lines of some breeds are only very fertile as young males and once fully grown are more miss than hit. This ideally shouldn't be the case with quality purebreds but it's not uncommon, so it's possible your rooster is trying to concentrate his limited resources.
You can lower their expectations by creating a temporary drought of mates, for sure, but be aware that sometimes rejection of an unwanted potential mate turns violent.
Also, isolating some hens from the group then later reintroducing them to the flock will create conflict, and sometimes permanent schisms. It will give you an idea, at least, of how aggressive your lines are under stress. I reckon it's better to know in advance and under controlled or at least supervised circumstances than to find out the hard way by surprise, which most people do instead.
It's also possible your male is just very paternally minded. Roosters that have paternal instinct can be very fussy about hens, and there's nothing less attractive to them than a hen with no maternal instincts. A rooster that chooses one hen to devote his energy to is generally a male with sufficient instinct and intelligence to be working towards creating a family, his interest is not restricted to mating at all, and prolonged failure of his chosen mate to produce chicks can lead to him trying to pair up with a hen that has chicks. My roosters always took note of which hens had chicks and which never did, being clearly attracted to the former and not the latter, and the non-mothers eventually ceased producing any fertile eggs whatsoever, because the roosters refused to mate with them. Which they mostly found a relief since alongside lack of maternal instinct most of them lacked the instinct to even want a rooster around at all. That was in a flock that had a gender ratio that peaked around 50:50, so the infertile eggs certainly wasn't for lack of fertile males getting around. All the boys wanted the maternal females, and nonbroodies were unwanted.
Some roosters are stressed by an overabundance of hens, because they retain sufficient wild instinct to try to bond with an alpha hen and concentrate their time and energy into the full time job of protecting her, finding her the best feeds so she can make the best eggs and therefore the best offspring, finding her nesting places, and then helping rear their chicks. If your male is like this, feeling overburdened by too many females, he may be actively driving the unwanted ones away. It can be as mild and subtle as a nasty look, or suddenly turning around and lowering his head at a hen that's trying to follow him, very brief and nonviolent incidents which you'd never see except by chance, because they only need to happen one to three times for most chooks to take a permanent hint. Chickens are pretty good at giving the 'evil eye' and it doesn't take too many repeats for a chook to take it to heart, so to speak, and permanently avoid one another.
The only males I've seen prefer more rather than less females were those that didn't retain sufficient instinct to provide for the hens, and even then they had favorites, they just liked to be surrounded by a crowd of females they often never mated with, lol. But they lacked instinct to the point that all they were good for was fighting, mating, and crowing. Which is fine if you're after certain traits and the familial instinct is not one of them, but not ideal for me, since I prefer them to raise their own.
Another possibility is that the hens laying the non-developing eggs have comb/wattle/face coloring at the moment that indicates they're not 100%, so he's leaving them be. Some roosters won't mate with a hen with a pale face, since generally that indicates infertility whether through illness, immaturity, or whatever.
The eggs are of different shape and color (all brown - some light brown, some dark brown, some big, some small, some elongated).
The 'elongated' bit makes me wonder, how elongated exactly? Hens with health issues can sometimes produce very elongated eggs and they're rarely capable of development. Also, what's the shell quality like, both externally (good 'bloom' and even surface, smooth, not dimpled or flawed) and internally (doesn't show patchiness or weak spots when candled)?
The ones that were not fertile, you could practically match them up in 3 different groups as to size, shape and color, so I am supposing that would indicate there are probably 3 hens that he is not interested in anymore.
Depending on what the eggs look like, it could be three hens that are not physically 100% rather than just infertile eggs due to non mating.
Do the dud eggs begin to develop at all?
Also, do the hens remain together or split off into groups?
Our rooster has a favorite, they are always together and he has another one that we have seem him mate with. The other ones, we are not sure of. If we separate him from his 2 favorite hens, do you think he would go ahead and once again mate with the other ones or do you think perhaps the "love has died" for them.

My husband and I are pretty new at this but having a blast - have totally fallen in love with raising chickens.
He probably would mate with the other ones if you isolated them together, but there may be very good reason why they're not currently mating. I have tried in the past to breed roosters and hens that did not have any interest in one another, and after a prolonged effort to achieve this, all it resulted in was poor quality offspring that I did not keep because they weren't worth it. Conversely hens and roosters that take a real shine to one another tend to produce inexplicably good offspring, so even if I did not originally intend to breed them or keep their offspring, I now do; they tend to be worth it.
A successful breeding can also be defined as one which results in offspring superior to either parent, not just one that results in offspring of any description whatsoever.
If your rooster has 3 hens too many, another rooster should appreciate them. Their genetic potential is wasted if forcibly tied to the wrong male through lack of choice.
He might not be a bad match, there's so many potential causes of the infertility, but it's worth considering keeping multiple males. If you keep them free range, and the hens already isolate into two groups it shouldn't be a problem to have three hens per rooster, but if you don't free range them, or if they remain in one group, given your rooster's solo-male lifestyle, there could be serious issues, since his tolerance levels and experience are likely too low to tolerate another male.
I don't know what you keep your chooks for or what your setup is, but personally I like to grow some for meat as well as the other uses (eggs, breeding projects, etc), and I like them free range, and in an inclusive flock (all together, no permanent segregation). So I don't want a flock that must be kept separately caged lest they kill one another. I need my chooks to remain peaceful, so I won't keep less than two roosters at an absolute minimum, because they easily develop unrealistic perceptions of their own capacity in the absence of competitors, and often lose the ability to defuse potential conflict peacefully. They can fail to develop the sense/instinct to detect that they can't win a given fight, or lack the body language necessary to show submission and coexist peacefully. The same can all happen to hens too, of course.
Inability to either perceive or accept submissive behaviors were two of the main instinct/social malfunctions I targeted in my initial purge of bullying/aggressive mentalities, but I did have one hapless male I had to get rid of because he lacked the ability to realize he needed to show submissive behaviors, because he couldn't win. He came from a solo male background.
Social tolerance is partly learned and partly genetic, but if you want to expand your breeding operation or think maybe you'll want to keep more hens and roosters in future, or rear another generation with their parents, you're going to need your current mature male to be tolerant of other males. This can be achieved by growing his own sons up around him, it's the gentlest and most successful method of introduction into a multi-male society for roosters reared in only female company. Once he's shown ability to coexist with other males you have options for 'unwanted' hens and more breeding and genetic opportunities.
I don't know what your setup or aims are though, there's a lot of complexities unable to be guessed at.
Best wishes.