Nope there is a relation. At least in the way angels are handled. Though instead of the Archangel Gabriel being the bad guy, here it's Verchiel. I think though that this story is more complicated that the Prophecy films and between those films and these books, I like the books better. If you did like the Prophecy I recomend you give this a shot. Chances are you'll like it.
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Yeah you could definitely see some similarities. Verchiel referred to humans as "monkeys", as Gabriel and the angels did in the Prophecy. The Nephilim was part of the plot in Prophecy 3: The Ascent. It is indicated that the Nephilim had a scent, though in the Prophecy, angels all had a scent. Though the Nephilim did not redeem Gabriel in Prophecy 3, Gabriel was redeemed and it is suggested that he was redeemed by assisting the Nephilim (Danyael). Though not really a direct similarity, probably, in both Fallen and the Prophecy, Lucifer/Satan pretty much stays out of everything, only appearing in the first Prophecy to restore balance at the end, and a brief appearance at the beginning of Prophecy 2. There is the whole misunderstanding of God's plan in both films as well. The Punisher, in Fallen, gradually came to understand God's plan, as did Gabriel at the end of Prophecy 3..."the word burned brightest, and for a moment I was blinded."