Why you would lose your arch when slightly above parallel but be able to maintain it when doing a full squat makes no sense to me at all.
For squat depth, go as low as you can while maintaining a neutral spine and without tucking your tailbone under (which would change that neutral spine, huh). That depth will be different for each individual based on their own mobility and anatomy. If you can't get to parallel without changing your spine, then in addition to squats you should include some prying (sitting in the bottom squat position to work on opening the hips) and other mobility/flexibility work.
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Lisa Holladay, CSCS
Exercise and nutrition play equal roles, and the motivation and discipline to stay consistent are really the glue that holds a program together.
--Alan Aragon
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