Loosing 40,000 men was not catastrophic, look at some of the WW I battles.
And the Germans had several million men in the Army.
Sinking the first wave was not all that costly to the German army. It would have pretty much wiped out the functional German navy though.
Letting the Germans land the first wave and then sinking the 2nd wave would have roughly doubled the German casualties without a lot more losses on the British side.
German 1st wave would have to surrender in 3-5 days due to lack of supplies, like food and ammo.
German 1st wave doesn't have a lot of heavy weapons. Sort of a reverse Dunkirk, Few tanks and only light artillery.
Germans still have the bulk of their panzer divisions. Only a few battalions in the first wave and 8 or less in the second wave.
Getting rid of some of the Pz Is and IIs may have done Germans a favor?
The German expected a much harder and longer battle for France with higher causalities.
Sea Lion was another gamble, 50-100,000 men lost and winning was one thing. Loosing 60-100,000men and British still holding southern England was another story.