Hello Turbo DV8,
The first few charge/discharge cycles are designed to bring the cells back up to decent operating condition. No special care or observations are required during this part.
I seem to recall that the top off charge is applied in the cycle mode, but I don't know if it is applied during the refresh and analyze mode. There may be information on this in one of the C9000 threads, or you can run a test and see if the voltage climbs during the rest periods. If the voltage increases during the rest period, the cell is being topped off.