Only US metal flight miles brought from US Airways are counted in AA program.
This effectively means that any miles from US acquired airlines, and any non-flight miles are discarded.
your miles didn't get discarded...they just didn't count towards AA million mile status, which is separate from your redeemable miles. You got the miles once from the US DM program and didn't lose anything, and in fact spent them, and if you didn't spend them, they're now AA miles, just not AA million miler miles.
Don't expect to get anywhere with AA simply because, as you said, you got the wrong impression of how US miles would work in the AA million miler program