Probably the best and safest way to store your batteries is to leave them on the bikes, in a charged condition, and recharge them every month or so. Li Ion batteries don't like to be stored uncharged, so putting them in a box for months may not be good for the batteries. Keeping them on the bike prevents accidentally shorting the terminals, which is probably the single most dangerous possibility. Plus keeping them on the bike ensures air circulating and makes it easy for you to check condition and recharge as needed. FWIW you probably want to keep them charged in the mid range of 20-70%, letting them slow drain then topping back up.
Ultimately the best protection with Li Ion batteries is choosing the source carefully, and avoiding low quality, cheap batteries and knockoffs. Then keep a weather eye for any recalls.
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