"There are flies above the cows."
Translation:יש זבובים מעל הפרות.
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.
Do any modern Hebrew speakers think we could use prolepsis here? Either יש זבובים מעליהן הפרות or perhaps ישנם זבובים מעל הפרות. Muraoka (Modern Hebrew for Biblical Scholars, xxvi) says is a highly frequent feature of modern Hebrew. I didn't try it with מעליהן, but I think it probably will be accepted.