...for most of the time the E-D is undergoing a cycle, the Bozeman is leisurely cruising in the 23rd century and not repeating anything. The Bozeman only participates in the cycle after arriving in the 24th century!
How do you know?
Because the collision between the two ships is the only thing that causes the loop. We know this from the final scene - the Bozeman
comes through, does NOT hit the Enterprise
, and thus the cycle is broken.