Inasmuch as theft is a serious matter, are you sure the money was stolen or, as your message title suggests, is it some sort of unintentional "screw-up"? Instead of theft, could it be the result of underestimating future repair needs during the budgetary process?
If you believe it was stolen or otherwise illegally used, discussions with the police and NYS Attorney General would appear to be indicated.
Do you know when the money was first thought to be missing? Your message implies it occurred around 2008. If so, over the last six years the depleted reserve account would be expected to be noted in bank statements, treasurer reports and/or annual budgets. If you haven't done so already you may want to request the opportunity to review such documentation.
Also, when we establish organizations similar to yours we put accounting techniques into place that help guard against one person having full access to funds. You may want to inquire as to the techniques your condo employs.
Hopefully the situation you face can be resolved without a significant maintenance charge increase.