Board Thread:Syndicate general discussion/@comment-81.100.215.185-20151222194052/@comment-13471981-20151222201453

What bonuses are we talking about here? Cause you can replay every memory in Syndicate by accessing the Progress Tracker in the pause menu, to get full sync objectives if you missed them. 

If you do want to start over from scratch completely, I think you'll need to wipe the game data. I'm not the best person to ask on this, but I'm sure if you check elsewhere on the internet, you'll find a guide or something to help you with this - I imagine others will have run into the same issue as you have. Good luck!