I had the same Problem like a dozen times, got fed up and contacted Ubi support. They didn't know what to do so i did my own searching. I found that if recruits use either throwing knives and/or gun, it will fail the sync. so either be lucky to get them to use hidden blade, or use arrow storm. worked for me. I also got 100% when I was on Ground level, maybe that helped or just lucky since they used Blades. They even got detected, didn't ruin the sync.
Brotherhood is kinda queafy because you can desynchronize in the middle of a memory and retry at a checkpoint, but once you fail full sync you have to start back at the beginning.
Use arrow storm for each set of followers. If by the time you get to the second or third set arrow storm hasn't recharged, find a way to desynchronize like letting Micheletto get too far away or commit suicide by jumping, and it'll start back at the last checkpoint but with the meter at the level it was at when you desynchronized.
It's cheap, but a poorly designed level deserves no better.