Did the embryologist look at the semen before using it? If you sent her to a clinic, that is what they should do! Then you know the semen is good before you put it in. We had a flush with 12 UFO (unfertilized objects, or eggs... Common term out here). Vet blamed it on the fact that the donor came up with accessed feet right in the middle of the flush cycle, so she was in pain. I'm not so sure the semen was not bad. Next time that gal gets flushed she will go to the clinic (this flush was done in house, so we bred her and could not look at the semen). If she gave you unfertilized eggs, she is doing her part in the flush, unless there was a problem with the eggs.
Regardless, good luck. If you do not try to flush again, you will likely regret it when you lose her. We flushed a cow in October, and she calved in June that year. Our vet wanted to wait till it cooled down, because he said we get better results. California is a lot hotter than Missouri!!!