So I realized I never got my trophy for finishing the campaign and I still wanted to get the intel and stuff. Loading up the mission select I realized that a little over 1/2 through it acted like I didn't finish any of the missions. If I go with "continue game" it starts on the last mission. So I started on the mission select where I said I need to pick up and went 3 mission in. Save, quit, and then check the mission select...still the same problem.

I check a couple of forums and see a few people say the same thing but mums the word from Activision and Sledgehammer (which hasnt responded to anyone who isn't patting them on the back). Anyone else experiencing this?

I played the game a bunch yesterday and quit and went to sleep. Then I continued today and it had kept my story progression when I resumed the game but deleted my upgrades. The chapter select screen only showed that I had played the first mission. The Exo challenges were still counting up so I guess I can't even get all the upgrades anymore.

@terjay: I bet I lost my upgrades too now I think about it. I know I got the next to last trophy for EXO upgrades but I think when I went back to it for a third time I only had 13 or 14 so that's not right. This is kind of aggravating especially with all the other nagging issues I've seen.

So, as an update, a random person from Activision support got in touch with me on Twitter. We went back and forth exchanging some information about the issues I was having in the single player and it ended with him providing me this link and telling me to wait for the upcoming patch.

https://community.sledgehammergames.com/community/sledgehammer/blog/2014/11/07/excitement-from-call-of-duty-advanced-warfare-launch-week-and-updates-coming-soon