Similiar problem and still not resolved.

In April, I booked two TATL BE tix for 200,000 (yes, I got the lowest # of miles!). A short while later I changed my outbound destination, for a change fee and NO miles. Delta took another 200,000 miles (50,000 each way per person) yet only redeposited 100,000. I've phoned twice and spoken with the SkyMiles people. They agree that I am owed 100,000 miles but they can't seem to do anything while I'm on the phone (for 30 minutes) and my case is being passed on to an internal department (now for the 2nd time).

The explanation the rep gave is that all my tickets appear closed. Typically in cases like this there is an open ticket with the missing miles attached to it. But in my case she said the miles have disappeared into the ether.

Both reps have been very courteous and understanding. The latest rep suggested I check again in two weeks and call again if the miles have not shown up.

This is mildly frustrating and I am not left with a high degree of confidence the miles will appear anytime soon.