Long story short, I played the first mission one time before I logged into my IO account. The challenges I completed before I logged in have disappeared. It shows that I have not completed them, but they are not available to be completed. It seems that they wont award the challenges if you are offline to prevent cheating, but now that I am logged in why can I not re-complete them? At this point it would not be a big deal to wipe my saves and start over, but is there a way of doing this? Also, does anybody know if you progress from Season 1 can be applied into Hitman 2?
Regarding the locked challenges, you can go to the Official HITMAN 2 Technical Support Thread and submit your issue there, where IOI staff can help you.
Regarding applying Season One content to HITMAN™ 2, no, you can’t transfer your progress.
This is still a PC issue as well.