Have you tried the TK feedback form? I had some SK flights that failed to process to my TK account. The normal claim form failed but a detailed feedback form with ticket details, BP scan and passport scan (believe it or not) eventually worked.

Your case sounds more complex than mine. By the way, several years ago I had some random miles appear in my SQ account for a flight I didn't take. Some time later the miles were reversed. So mistakes definitely can happen.

Good luck.