I don't know for sure the lifecycle of Babesia but I did know Lyme which was an every month event like clockwork at the start of my treatment my symptoms flared or got worse. That went on several months and then stopped for me.
Yes the bugs die off and then a new group cones to life and the cycle starts again.
I had Lyme and babesia, and while I could sense feeling better and worse at various times, the overall picture of gradually getting better was more significant ... and, in my view, more significant.
The different infections have different life cycles (for example, search 'lyme disease cycle' online) that overlap and mix it up so that it's often not clear which infection(s) are causing this afternoon's misery, as opposed to this morning's misery. Don't make yourself crazy trying to time the little creatures -- think more of long-term trends. There are too many variables to chart.