I solved this same problem; my wife and I play the game together, but I wanted to do a solo mission without messing up our achievements.
I did it by using Steam Family Sharing. They allow you to register a second Steam profile on the same computer, and then share games between them. Logging into my new account, I requested access to the game (which I granted to myself) and it started up with a fresh set of achievements.
When I want to go back to the other set of achievements, I use the other profile.
Abbey Games has a new community and forums! Come on over to https://community.abbeygames.com and don't forget to mention your old username! The old forums will remain available, but read-only.