Yepper, bidirectional cylinders have fluid on both sides of the ram. Only way to get it all out is to dismantle the hydraulics piece by piece. Besides, considering the volume of the FEL system vs sump, not that big of a deal.
Where the concern comes in is when you have hydraulically driven implements that you use on different tractors. That's where the problem lies...old implements having been driven by old tractors not requiring today's lubes, or full of water from sitting out for years in the weather.......