I didn't collect many side missions like challenges, nests, posts, and black disks, only those I encountered along the way.
Drop along the path: C:\Users\Your username\Documents\Activision\Prototype 2
There shouldn't be any Cyrillic characters along the path, otherwise the save won't work.
I'll also add a guide in case you want to replay or start NG+ regarding the trap mission.
Before the mission itself (before you accept it (step on the blue circle)) you need to go to the Task Manager, click on the Prototype 2 process, click "Details," then click "Prototype 2" again, and there will be a button to set affinity. There, you need to leave any one processor (for example, CPU0). The game will lag during the mission because only one core will be running, but the mission will still count; this is a developer error.
It might not work the first time, but it will! Second point: If the picture jerks when you move the mouse, turn off vertical sync in the settings; it helped me.

Author: Swolix