HV Pulse Blocking with Common Mode Choke
Lets assume each side of that choke has 1pF parasitic capacitance across the windings.

Lets assume the dV/dT of the pulse is 25,000 volts in 15 nanoseconds.

What is the current thru the 1pF?

I = C * dV/dT = 1e-12 * 25,000 / 15 e-9 = 1e-12+9 * 25,000/15 = 1.67 amps.

Can your "protected" side survive with 1.67 amps arriving, during that pulse?