I think this is actually two questions: "Why were those flags declined?" and "Should I have done what I did?"
For the first one, I believe (based on things I've seen mentioned on meta.se) that if a moderator deletes comments that have flags pending on them, those flags are auto-declined. In this case, you should see your declined flag count go up but there won't be any way to see those flags in the declined flag list. That would be a hint as to what happened.
For the second one, your approach is probably not the way to go. As explained by Shog9 in this meta post:
But if removing the comments requires a moderator to review an entire comment thread and pick out which bits are no longer relevant, or verify that an edit has indeed obsoleted a good many of them... Then multiple comment flags don't really accomplish much. Just flag the post, summarize the problem, and let the moderator deal with it. This is especially true when the bulk of a thread should be removed.
In this case, if the first comment flag was enough to clue the moderator in that the entire thread was out of hand, then having a second comment flag isn't helpful -- it's just noise. In that case, the remaining 12 flags were redundant, and got declined because there was nothing left to "do".
(You could argue that perhaps pending flags should be approved when the comment is deleted, but that doesn't appear to be the case for whatever reason. You'd have to ask on meta.se if you really wanted to know why.)