I had a 100k Biz Class US-Europe round-trip and changed the return to one I found available online for 100K a couple weeks back, though the domestic connection was in Economy. The agent changed it no problem. Then I checked my account just now and they credited me 100K but charged me 125K for the new itinerary.
I wrote to "Contact Us" specifying the PNR and suggesting that maybe they hard charged me a full 25K for the domestic economy segment, instead of considering it part of the entire 100K biz itinerary. Here are some quotes from the response from Contact Us:
"Thank you for your email to Delta Air Lines regarding SkyMiles award ticket. The mileage required can vary depending on the route, cabin and on the award level of the flights you select. The exact number of miles required will be known once you select all the flights in your itinerary. Please be aware that the mileage redemption rate is subject to change until the award is redeemed and ticketed ... we recommend you review the new SkyMiles Award Mileage Charts ... thank you again for giving us an opportunity to respond to your concern. We highly appreciate your Platinum Medallion loyalty to Delta and look forward to the privilege of serving you soon."
So I called the Plat line and the agent recognized in two seconds that it was mis-ticketed and that they had charged me a separate 25K for the domestic connection (no stopovers were involved). After being on hold for about 5 minutes he said it was fixed. But then he double-checked that I was only being charged 100K, and lo and behold the system was still having me charged 125K. He then said he "tweaked" something and that fixed it, and the 25K has been refunded to my mileage account.
I wrote back to Contact Us to tell them that it had been indeed misticketed, but I don't imagine this will register.