Peter,
the warning only pertains to fully charged batteries. If you put a battery on the charger, the charger needs to check whether it is full or needs to be charged. It does that by trying to pump some charge into the battery and sees how it reacts. If you do that repeatedly on already fully charged batteries you may eventually damage them.
I reckon if you frequently recharge only slightly discharged batteries they might need a calibration run more often. The charger keeps track (on an in-battery chip) how much it has pumped into the battery, and the battery keeps track of how much is has delivered. Based on that, the batteries full charge capacity can be monitored, and compared to the nominal full charge capacity. This shows the battery's decline and gives rise to the battery lifecycle display (which is way cool!).
If only small amounts are discharged and recharged, and a large amount of charge remains untapped, this monitoring is less effective, and the charger may need to do a full discharge/recharge to get a good bearing on the batteries present full charge capacity. Same is true if a battery isn't used for extended periods (because it keeps aging).
I've got two EN-EL4's and usually run them down until the camera tells me to change them. I have yet to be asked to do a recalibration.
I think the EN-EL4 is one of the best features of the D2
Cheers
Steffen.