Destroying the PDC...there are two ways to do that. One removes the PDC with no wreck and the other (Destroy) leaves a wreck in 6.10 (the version I use). It may have changed, but I destroyed a PDC by accident and then was able to salvage the wreck it was the first action my salvager did.
Refit is something that you should do when the ships get minor updates. If you are basically rebuilding the ship you are often better off to scrap the ship and build it new. This gives you the components from the old ship that you can then either scrap or reuse. The whole scrap and rebuild can be astonishingly fast, especially if a lot of major components get recycled. The Spaceframe Renewal Program the NCC launched did a great job and the ships were back in service quickly.
Where Refit really sucked was in updating my PDCs...there the cost and time of the action was greater than a newly constructed PDC. If engines are getting changed I'd almost be tempted to scarp the ship and rebuild it because I find Galacite in short supply and being able to recover from the old engines yields a fair amount of the mineral. But as with many things if that makes sense for you depends on your exact boundary conditions.