Does it alter battery cycles, the battery or the hardware in any way if I keep an iPhone 7 stored in its box for 3 months without use?

The device has been switched on already, the battery was at 60 percent before it got turned off for a long time. Is it bad? Will the battery lose some of its capacity to retain charge? Please explain.

No it should be fine. At somewhere near 50% they can last for years.

They should not be held at full charge or left flat for any length of time, as either can reduce life or wreck the battery - but near mid charge is ideal, the makers recommend it for storage.

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