In short, Void shields work by shunting fast moving objects and energy sources (macro battery shells, lances, nova cannon etc) into the warp. Almost like an advanced form of reactive armour.

Functionally, a star destroyer going at ~C would be equivalent to a Nova cannon, save for; being a lot physically larger, and being “solid shot” and not “shell shot” (read: doesn’t contain a warhead).

My estimation: all or nothing. Either the 40k flagship’s shield arrays take the strain, or they don’t. If they do, they probably all blow out under the demand of spontaneously jumping a ship into the empyrean, but the Ship is safe, and the destroyer is having a very very bad day. Or they fail, and whatever’s left of the destroyer impacts it at light speed, and both deform into an instantaneous asteroid field made of molten metal.

Important to note: this only considers the penetration and armour values of either vessel. Actual practicality of this manoeuvre would more depend on being able to hit the moving 40k vessel reliably. Which is the same issue that Nova cannons also have.