I haven't been there myself, but I wouldn't mess around with fluid in the lungs.
When my little guy was just a month old it was discovered that when I fed him, the breast mild was going into his lungs. The doctors were very concerned and addressed it immediately (ran tests, x-rays, etc). He was immediately switched to the bottle with a thickener so this wouldn't happen again. The nurses were very adamant that he not be fed any other way and that if he were we might soon find ourselves in the emergency room with pneumonia.
Fluid in the lungs is not something to take lightly. It's very possible the he prescribed a higher does as a precaution because of the fluid in the lungs. I would continue with the dose he prescribed and call your ped in the morning.