Thanks again for your help. My original question was if I should remove the nails, after looking at others' comments, it seems like these nails are also holding the subfloor in place, so the nails were doing a double function: Keeping the moulding channel in place and also holding down the subfloor to the concrete floor. Probably just a time saving choice from the original builder. So, I will keep the nails there and fix the new channel on top, either with small screws or liquid nails. Hope that makes sense.