As I mentioned above - Norway and Crete both illustrated during the war the number of sorties that needed to be flown in what aprticular circumstances for the RN to lose ships...and THIS time they'd have to be flown within reach of Fighter Command's Eleven GroupAlso, given enough ships as targets, it could take much if not all of the luftwaffe sorties to sink or destroy all of the RN flotillas. Using the 1944 Pacific campaigns as a guide, USN carrier based attacks took close to a 1000 sorties to sink IJN flotillas of 8-10 destroyers. Those are small, dedicated strikes by the elite of the USN carrier based air arm, using planes and tactics designed for just that sort of attack. The Luftwaffe is not that far along and would be forced to use a lot of medium bombers at low levels, dropping level bombs.
One thing to remember is...the RAF would have a much easier time attacking the "invasion fleet" from the air than the LW would have attacking the RN. The LW would be attempting to sink fast-moving destroyers firing back at them...the RAF will be bombing slow-moving cargo ships and river barges rolling in the unacustomed swell Not quite fish in a barrel compared to what the LW had to do - but close!!!