I have been told by a mod to post this here in the bug forum. I had this issue with another mare before but wasn't on laptop to take screenies before ultimately deleting the embryos altogether.

I had a mare die without offspring. Since I can't always prioritise my EEE girls, but want to preserve them, especially if they still have my old lines from my first stable in their pedigrees I decided to take some embryos instead. Works with straws, right? Even if the horse is a gelding. Well, I had to find out that the embryo just sort of vanishes from the list if the mare passes without offspring, but still exists in a limbo - unimplantable though, untill I destroy it.

I made some screenshots to illustrate my point

here's the list of embryos with the potential mom's name missing:

and here is her name, visible when I go to the "destroy embryos" tab:

Next we are in the breeding center, as you can see the embryo DOES show up and I selected a surrogate mare and clicked on "implant":

However this is the message I get when I try to implant the embryo:

So as of this moment there is no other solution for me than to destroy the embryo as I cannot interact with it in any way after the mare has apparently been erased from the game (from old age, she was not sent to the FR) and cannot be revived. I don't know if this can be fixed in the future, or at least awareness be raised for people collecting embryos, since there still was a minimum 15k fee for each embryo I've lost so far, even with the golden token.