"There are flies above the cows."
Translation:יש זבובים מעל הפרות.
Interesting question. As a native I can say it sounds unnatural.
They variation would be used for a definite subject, as in
הזבובים נמצאים מעל הפרות
I can't point out exactly why it's wrong, though. You would be understood if you said it.
I think because one noun is definite while the other is not. You can get away with saying זבובים נמצאים מעל פרות, as a general rule flies can be found over cows. Or you can use the sentence that you proposed, as the two nouns are definite. It appears that using one and the other doesn't work.