As far as the physical battery is concerned, it doesn't matter.
The main thing is that you do it after flashing a new ROM or switching back to a CWM (nandroid) backup.
Here is the science behind it...
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Originally Posted by Entropy512 on xda
This is standard for Lithium-Ion batteries (of most chemistries - there are exceptions, but our device is not one of them.)
The standard charge cycle for a Li-Ion is as follows:
Constant current (aka current-limited) initially, until battery voltage reaches approximately 4.2 volts.
Once the battery hits 4.2 volts, it is constant-voltage (battery his held at 4.2 volts)
Charge termination is done by monitoring the charge current in the CV phase. Once the current drops to around C/10 (e.g. 165 mA for most GSIIs), the charger is shut off. I need to double-check this number.
As the original post hinted, and I have confirmed by reading kernel source - this advice is applicable to most HTC Android devices, and other devices (such as the Galaxy Tab 10.1) that have "coulomb counter" type fuel gauges. These measure the current in/out of the battery periodically and sum it up - Slowly, their estimate of state of charge will "drift", which is why they occasionally need to be recalibrated.
The Maxim fuel gauge IC used in first-gen GalaxyS devices needs no calibration, and in fact, is designed specifically to be "convergent" rather than "divergent" - i.e. if it is initially "uncalibrated", it will converge on a correct state of charge estimate after a few hours, regardless of initial conditions. See MAX17040, MAX17041 Compact, Low-Cost 1S/2S Fuel Gauges - Overview
The MAX17042 in the GSII (I9100 and I777, probably SPH-D710 also) is an improved version of the 17040. While it does, unlike its predecessors, have a current measurement function, it is not used right now (see kernel sources) - so it's functionally almost identical to the 17040 for us.
This fuel gauge assumes the battery is in a "relaxed" state initially - so ideally, if you want the best "calibration" - pull the battery for an hour or so, so that it is "relaxed". If this seems to long to you - overnight idle drain will be low enough that any State of Charge (SoC) estimates will converge, regardless of initial conditions."
[TIPS] The Best Way to Calibrate our S2' Battery ! [No root needed, Very accurate] - xda-developers
So, I hope that's all very clear to you now.