If you do delete them using sm mode, go to your mineral stockpiles and add the approximate amount that you would get from scrapping them (1/3). If you want to see how much minerals and money it took to build them go to the industry tab and select the pdc in question. The minerals used will show up in a box on the bottom left of the screen.
There is also a long standing problem of refitting pdc's. You can tell aurora to do it, but nothing actually changes. The easy workaround for this is to que up the changes, wait till they are done, then go into the ship design screen and change the design (you will need to have sm mode running, unlock the design, make the changes and then relock the design.) Once you do that go to the F6 screen and select each individual ship to have the design be updated. People often use this trick if they made a really dumb mistake in designing a ship, like forgetting to have any fuel on board, or a scout ship with no sensors, ect.
Brian
