Dont you people tire of these fantasies. Anyways lets indulge your fantasy.
Your basic mistake is in believing that S400 will working alone in isolation , but in reality it will just be another part of multi layered air defence network.
Now what will be the components of this air defence network.
AWACS, Aerostat Radars, Surface based Radars, IAF fighters, S400 SAMs, Barak 2 SAMs, Spyder SAMs, Akash SAM and lastly Green Pine Swordfish radar along with AAD and PDV for missile defence.
At the fore front will be AWACS, which will detect your 48 drones as soon as they take off.
Aerostat Radars will pick up cruise missiles as well drones soon after launch.
At which point IAF fighters will be scrambled to take on the drones.
A drone flies at a speed of 200 Km per hour, A cruise missile at 800 Km / hr, where as fighter flies at speed of 2000 Km /hr.
If launched from just with in 100 Km inside Pakistan, A drone will take 1 hour to reach a target 100 Km inside India, but it will take only 10 minutes for fighter to reach the drone, but of course it can launch its AAM much before that.
A Su 30 MKI in a purely air defense configuration can carry 10 R-77(100 Km range) and 4 R73s (30 KM range), that is 14 missile per aircraft.
Guided by AWACs Just 4 Su -30 can bring down your entire fleet of 48 drones, within 15 minutes of takeoff and well within Pakistani airspace.
Now all that remains are your 12 cruise missiles, here you have multiple choices AAD, Barak or S400's 9M96E missile(which specializes in shooting down low flying and stealth objects. And Even if couple of missiles are able to strike their targets, the raid itself would be a failure.
Wing Loong is slow and big, it is a sitting duck for fighter or even long range SAM.