For example the Remaining Active Relative Capacity register:
The ACR is backed up when the RARC crosses a 4% boundary. Meaning, when charging or discharging, when the RARC crosses 100%, 96%, 92%, 88%, etc it will be backed up.
It is possible that when you initially charged to full, a 4% boundary was not crossed (if it was near full when the charge started) or if the RARC was above 100% when starting.
Please see Parameter EEPROM—Block 1 in page 30 of datasheet.
The Cycling listed in step 2 would definitely cross many 4% boundaries.