The following was submitted by a knowledgeable customer. We have not tested this process, although it worth a try.

Purpose: confirm when a new higher-capacity cell has settled in, using the USB-C top-off as the signal. This does not calibrate the on-screen meter — that stays voltage-based and unreliable with this board — it verifies the cell, not the gauge.

What you need:

30-pin wall charger + cable
USB-C charger + cable

The signal: each cycle, the 30-pin brings the cell to the iPod circuit's termination point, then USB-C tops off past it to the board's higher endpoint. On a fresh pack that top-off takes a while; as the cell settles over the first few cycles, the top-off gets noticeably shorter, then stops shrinking. A top-off that's stopped getting shorter is your "settled" signal.

Procedure (per cycle)

Full charge via 30-pin wall charger, uninterrupted. Overnight is fine. Wait for the on-screen "charged" state. Use a wall adapter, not a PC port that may sleep.
Top off via USB-C until the board LED goes green. Charge on one port at a time — never both live at once. Note roughly how long the top-off took relative to the previous cycle.
Use the device normally until the next charge. Mixed real use is enough to exercise the cell for the next cycle — no forced deep drain needed.

Completion criteria: when the USB-C top-off stops getting noticeably shorter cycle-over-cycle, the cell has settled and further cycling buys nothing. Community reports of big-cell mods "becoming accurate after a couple of cycles" are describing this same settling.

What this won't do: the on-screen icon stays voltage-based — long red, uneven drops, "charged" before it's truly topped off. That's inherent to a voltage meter plus a second charge controller the iPod can't see, which is why the board's LED is the charge indicator, not the screen.

Reference links

iFixit — 3000 mAh mod, indicator accuracy after a couple of cycles: https://www.ifixit.com/Answers/View/550621/
iFixit — ~3.5 V low-battery cutoff behavior: https://www.ifixit.com/Answers/View/11645/

Troubleshooting — deep-drain recovery ("no turning back" floor)

If the device is drained past its firmware low-voltage cutoffs — e.g. via the stopwatch method, which coasts under the video/audio safety trips — the cell can drop low enough that the 30-pin won't start a charge. To recover:

Plug in USB-C for a short revival charge (~30 min worked best in testing; 15 min was marginal). This brings the cell up just enough to clear the gate.
Wait for the "battery very low — please wait" message. That's the sign it's back above the floor.
Switch to the 30-pin wall charger and charge fully, uninterrupted (overnight).

Note: this is a recovery path, not a routine step. Deliberately draining past the firmware safeties puts the cell into deep-discharge territory, adds wear, and doesn't improve the meter reading. Treat the floor as a state to climb out of, not one to aim for.

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Full Battery Drain — The "Stopwatch" Method, and Why to Avoid It — iPod 5.5 gen + Boxypixel MKII

Short version: it is possible to drain the cell past the iPod's own firmware low-voltage cutoffs by running a minimal load like the stopwatch. Doing so reaches a true "floor" that normal use never hits — but it drives the cell into deep-discharge territory, adds wear, and gains you nothing. Don't use it as a routine. This page documents what it is so you can recognize and recover from it, not perform it.

What the method is

Under normal use the iPod's firmware powers the device down when the cell voltage sags to a cutoff threshold under load. Running the stopwatch — an extremely low-draw, playback-free load — lets the cell coast below the voltage where heavier loads would have tripped the safety. The result is a deeper drain than the firmware normally allows, ending in a "no turning back" state where the device only flashes and shuts off, and the 30-pin won't start a charge.

The three drain levels / two safety nets

New-cell testing surfaces three distinct stopping points on a single full charge:

Level 1 — video hits red → firmware powers down. Highest cutoff, most reserve left behind.
Level 2 — audio + backlight past red → firmware powers down. Lower cutoff, less reserve.
Level 3 — stopwatch → drains past both safeties to the true floor. The "no turning back" point.

Why the stopwatch reaches a lower floor

This is the key thing to understand: these are not three different thresholds — they're one voltage cutoff meeting three different load currents.

A battery's terminal voltage sags under load, and sags harder the heavier the load. Video draws the most, so the cell hits the cutoff voltage while still holding meaningful charge — it trips early against real remaining energy, stranding the most reserve. Audio-with-backlight draws less, sags less, so it coasts a bit further before tripping. The stopwatch draws the least of all, sags least, and slides right under the point where the others would have cut off — reaching the genuine bottom.

So the gap between Level 1 and Level 3 isn't three safeties doing different jobs. It's the same safety firing against different amounts of voltage sag.

Why to avoid it

The firmware safeties are protecting the cell, not obstructing you. They exist to stop the battery entering deep discharge, where it can fall below the voltage at which it's safe to recharge normally. Bypassing them puts the cell exactly where they were trying to prevent it from going — which is why the 30-pin then refuses to charge and only a USB-C trickle revives it.
It adds real wear for zero gain. Repeated deep discharges shorten a lithium cell's usable life. And because the iPod's meter is voltage-based (not a learning gauge), the deep drain does not make the reading more accurate — you pay in cell wear and get no improvement in the gauge.
It's a danger-zone state, not a calibration step. A cell that the 30-pin won't charge is a cell that's dropped too low, not a cell that's been "properly calibrated."

If you land here anyway — recovery

Deep-drain recovery is documented in the main battery guide's Troubleshooting section. In brief:

USB-C revival charge (~30 min worked best in testing; 15 min was marginal) to lift the cell back above the gate.
Wait for the "battery very low — please wait" message — the sign it's back above the floor.
Switch to the 30-pin wall charger and charge fully, uninterrupted (overnight).

Treat this as climbing out of a state you want to avoid, not a procedure to run on purpose.