@HDMI1
Oh shit, the reason why he can't find Filo is because he's going to the wrong guy to buy the eggs. The Slave Merchant sold Naofumi the egg, not that farmer.
I think it's more the timing and the circumstances. Naofumi got Filo 1) from the Slave Merchant 2) by picking randomly from what is basically a gacha 3) a month after he had been summoned into that world, 4) after saving Riyute village in his first wave. In his earlier loop/s, Motoyasu did pick all the eggs from the gacha from the Slave Merchant, but he did that before the wave, so maybe Filo's egg wasn't there yet (and/or maybe the village being saved or something other event in the original timeline is somehow related to Filo's being with the Slave Merchant).
In any case, he's going to the farmer to pick up Yuki, Kou, and Sakura, since the timing is pretty close. Don't know if he'll pick up Kuro and the rest (the filolials from the 1st loop) from the Slave Merchant, though.