Is it permissible to take an increase on the amount paid as a down payment for the purchase of an apartment that has not yet been received after two years, due to the depreciation of the original amount's value in the real estate market and missed opportunities, and is Zakat obligatory on the original amount upon its retrieval, knowing that a portion of it was borrowed when it was paid?

The zakat (definition) on this money is not obligatory for you, as it exited your possession upon the seller's receipt of it. A new lunar year (hawl) for zakat calculation must begin from the time it returns to your possession. As for taking an amount greater than the sum paid, this is not permissible unless you incurred actual harm due to the seller's delay in handing over the apartment, in which case it is permissible to take compensation commensurate with the harm.