You are responsible for the security deposit. The fact that your agent stole it does not mean that you don't have to pay it back. The deposit was taken in association with a lease that clearly defines you as the landlord, so even if we were to assume that the irregularities in the second lease somehow made you something other than the landlord you would still be the landlord who took the deposit.

You have recourse against your agent, and you may also have recourse against the new company based upon its acquisition of your original agent's business. See Johnston v. Amsted Industries, Inc., 830 P.2d 1141, 1142-43 (Colo.App. 1992):
Quote Quoting [I
Johnston v. Amsted Industries, Inc[/I]., 830 P.2d 1141 (Colo.App. 1992)]Under traditional corporate law, the liability of a successor entity depends on the nature of the transaction which gives rise to the change of ownership. Generally, a corporation that purchases the assets of another corporation is not liable for the debts and liabilities of the seller unless:

(1) the purchaser expressly or impliedly agrees to assume such debts; (2) the transaction amounts to a consolidation or merger of the seller and purchaser; (3) the purchasing corporation is merely a continuation of the selling corporation; or (4) the transaction is entered into fraudulently in order to escape liability for such debts.

Ruiz v. ExCello Corp., 653 P.2d 415 (Colo. App.1982).