To the best of my knowledge, running the battery down to zero helps to syncronize the battery meter. I'm not sure if it does anything for the actual battery though, as most rechargeable lithium batteries can't be discharged below 3.6V without damage. I could be totally wrong, but I would imagine iPhones have some sort of overdischarge protection?
I'm not aware either way of anything stating that you should or should not completely discharge an iPhone to fix anything with the battery or battery meter. I can tell you that LiPo batteries have only a certain number of charge cycles in them. The good news is that if you charge a LiPo battery from 90% to 100%, you've taken off 10% of one charge cycle of life from it, not an entire charge cycle. Also, I've always been told to keep LiPo rechargeables topped up for best life.
The iPhone definitely has overdischarge protection.
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