I just checked it again this morning and it did the same thing. Even the books that I had subscribed too are missing from my pull list again. I guess I will stop by my LCS today to see if its screwed up on his end too.
Do that, because the LCS's that are part of the Comixology system determine your pull list by that subscription list. If it is blank, they will not pull your books.
I ended up dropping a bunch of titles because Comixology consistently dropped my subscriptions and my LCS was not always good about reordering the comics I missed. That and their ridiculous licensing system for digital comics have led me to seriously dislike the company.