Not judging at all but maybe this will help you see where some of the concerns are coming from. Your posts and site are not consistent, and often contradictory. For example:
-- You say your male, who you thought was too young “got her” 3 times that you know of. So, it sounds accidental, since you thought he was too young for breeding. But later you say, “. The 2nd stud "mine" I had purchased because he IS the one I wanted to use on her so I aloud them to mate,”
-- You say “My breeding females are between 4&5 lbs. (AKC Standards).” But your site lists the females weights as 3 lb, 3 ¾ lb, and 4 ¾ lb. You say you haven’t bred the smallest yet, but your site does project her to breed with the 2 ½ lb male in August. So….looks like 2 of the 3 are less than 4 pounds and your statement here was very misleading.
--Some of your practices do not seem in keeping with the Breeders Code of Conduct and Code of Ethics as described on our breed’s parent club site:
The Yorkshire Terrier standard as posted on the AKC.org site comes from the YTCA.org. There you will find their recommendations:
"
The YTCA’s Code of Ethics precludes the
use of the words “teacup”, “tiny specialists”, doll faced, or similar terminology
by its members, and for good reason." (I personally don't get bent out of shape at the mention of the words -- seem descriptive to me but they do make a person well aware that the breeder is going against the YTCA.)
-and-
"(Females weighing less than 5 pounds are considered by most breeders to be unsuitable for breeding.)"
http://ytca.org/faq.html#A (I don't think weight alone is a good criteria to define a breedable female. But again, this is the recommendation from the parent organization.)
-- You say you have been doing this for 12 years with no lost puppies or C-sections. If all mothers have also sailed through healthily then that sort of trumps the odds. But you also say that you hired a stud for one female, and it got with another female (are you keeping them safely separated?) that you did not even know was in heat (Are you keeping good records?). You then mated her with a second male (your own) intentionally, even though you claim you thought he was too young.
--You are breeding less than 4 pound females.
--You are using terms like teacup, and micro-minis.
--You also claim to have a burgundy and black female?
--Then the subject of the thread … a puppy retained for 9 days?? Was she not checked to make sure there was no retained puppy? Did she get the recommended vet check along with the puppies? The retained puppy should have been caught. Had that been a still born retained too long like that, your female could have died from sepsis/infection.
So, like I said, there really are some things that jump out like
red flags. That is why the thread is veering off track -- red flags and questions.
I can see that you love your Yorkies, providing them with their own room, a TV room and chamber music. But, when folks see things that we have been educated to look out for, it is only normal for them to be mentioned. You have been fortunate so far, but I would hope you have a vet check that little 3 pound female well before you subject her to breeding. See what the vet thinks about her chances of surviving. I just could not take that sort of chance.
As for the original question -- no, I have never heard of that and I searched through the books I have here and what I find is that they are usually all whelped at the same time even if bred days apart. I did find mentions of retained puppies beyond the first day, but nothing like 9 days later. So, you seem to have an anomaly. One that you will definitely need to get DNA testing on all pups to sort out.
If you do have the females well checked for breeding potential, all the genetic and infectious blood testing done, clearly no history of problems like luxating patella, etc… and the vet says they can safely have puppies …. then I think there are always exceptions to the rule. More important than being under 5 pounds would be all these considerations, their bone structure, and their own medical history. Good luck to you and that little miracle late arrival!