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Is it safe to charge in a case, better to open the case, or best to take it out completely?
Definitely, heat & deep discharge are the enemy of Li-ion/LiPo batteries - they can be charged at any point, and do not suffer memory. Best stored at low (not freezing) temperature with partial charge.
The "memory effect" is overstated anyway - in NiCd, the true memory effect needed precise repeated partial discharge, and recharge with no overcharge.
Overcharge would reset that memory effect, but overcharge can create a condition many call memory, where the secondary conversion results in a lowered voltage over part of the discharge curve.
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