Many of the issues you raise are not within the purview of the Labor Commissioner's Office. The only issue will be whether you are owed the commissions. As to the emails, I would use them. You should not be expected to dispose of any proof of your right to commissions. If the emails had other information vital to the company like formulas, customer lists and the like, it would be very different.
Good luck to you.
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Since the emails were authroied by your employer you are entitled to use them against their claims, without question. You have no need to subpeona them at all. The Labor Commissioner will not be interested in anything but whether you were paid. Trade secrets (customer lists) will be of no interest to the issues of whehter you were paid what you earned.
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