Yes! Your Hubway Annual Membership codes and day passes will still work with the Blue Bikes system. The only difference is when you sign up using an old Hubway 24-hour code, you will get a free Explorer Pass (a 24 hour pass that gives you unlimited 2 hour rides). More about the Explorer Pass here.
If you're having trouble redeeming a Hubway gift certificate or 24-hour pass, you can reach our customer service line at 1-855-948-2929.