"I was wondering if the HSA balance was less than the total contributions, what effect this has for him."

This issue relates to trying to get the amount(s) returned, and obviously, over many years and having spending, that isn't likely. There will be taxes and penalty (excise on the excess). This issue doesn't affect how the computations will be done, each year, for amount contributed and deducted, that should not have been contributed and deducted, including any earnings each year are also taxable.