All exercises for a particular muscle group utilize the same muscle fibers. 3 weeks is a long enough time frame to lose some of your gains. I agree with Clare, you should start over. If you're doing the 6 1/2 month rotation, you probably could do just one week of each set of workouts instead of two, then pick up with Meso 2 as scheduled after a ONE WEEK rest. If you're doing the 3 1/2 month rotation, definitely start over.
The difference in the Mesocycles is the intensity of the workouts. Faster reps requires fewer muscle fibers as you are using more momentum, slower reps requires more muscle fibers, but you are always utilizing the same muscle fibers.