Val becomes Filia's son. L-sama (I assume) sends down an egg with a reborn baby Val inside. I am sure that Filia will raise him as her own. In fact, the screen shots during the credits show Val's egg being cared for by Filia.

Now, let's think about this. Even though Filia is not Val's natural mother, she is his adoptive mother. After raising him as her son, will Filia and Val be inclined to date as lovers, once he reaches dating age? Personally, I highly doubt it.