It is not unusual to machine the backing off after RT has shown a failure.
It does require the consensus of the approving engineer - at least from what I've experienced. And it should be noted on the PQR so that if the PQR is used for another customer all conditions are made known.
What you may need to watch for is that the plate is not machined away to remove a defect that is actually in the test plate, and not at the root or in the backing. PQRs are done to provide mechanical test specimens but they also are supposed to demonstrate proper penetration, bead placement, and other data on how the weld was made. If a defect at the bottom of the plate is machned away, you may be masking a problem.