Hmmm, I think I may have misunderstood the question from the get-go.
There is the Void Shield Generator Building, VSG for short, the Projected Void Shield, PVS for short, protects units / buildings within radius, and there are units within the radius of protection, IE Orks.
If you target the VSG Building, while the firing unit is within the radius of protection, you wouldn't need to worry about the PVS, as you'd be inside it. If you're within 12", to benefit from the melta rule, then you're inside the radius, so no substitution occurs.
If you're firing a Knight's Melta Cannon, from 20" away from the VSG Building, then what should happen is...
Measure range to building [20"], place template, scatter. We'll assume a "hit". Determine that the range is outside of "half" for Melta Purposes. Replace effect on targeted unit with an attack resolved against the PVS, using single d6 for Pen, as the range was determined to be beyond half. Assuming a Glance or Pen,
This is mostly conjecture determine whether or not the field would be at least 25% obscured by terrain, to see if it gets a cover save. For example, there may be ruins split by the radius of protection, which would block LOS to the newly "targeted" PVS. This is conjecture, as the PVS has no "Facing" to resolve against, be it front, rear, or side. Since the check for LOS being obscured occurs after penetration rolls are made, I feel it is reasonable to now consider the Field the target, for LOS / Cover save purposes. We've substituted what's being damaged already, so makes sense to continue using the PVS for the remainder of resolution? If the cover save passes, the shield remains in place. If the save fails, the shield is depleted per the rules for PVS.
If the Knight's Melta Cannon was within 16" when it fired, and you scored a "Hit", I'd say you'd get to benefit from the Melta rule against the PVS, as at the moment of range check for melta, you'd be within half range.
Blech... I'd be sure to run that by your opponents before a game. The sensible thing would be to use the melta rule if you're within half range of the PVS, regardless of distance to initial target, but I don't believe that follows the mechanics of the game. It would be an RAI ruling, albeit one that makes sense and would probably have popular support if a poll was taken.