Sometimes we need a bit of patience, I think they have promised to fix everything affiliates included , though, they maybe lagging to fix stuff since sometimes moving to a new system does not always go according to the plan and deadline. How about give them until the end of this week. Who knows, maybe by tomorrow, all is okay and you have all your referral details in order and those link are fixed and functioning fine for you.
Aside from that, you are unsure about things, so definitely to jump in a conclusion is kinda out of the line, and I hope your affiliate details be fixed soon. It is good to protect our interest and normal to worry but things will be better if we have more patience .