Is zakat obligatory on the entire borrowed amount invested in a project, or only on the invested portion, and what about the retrieved portion of the loan, is zakat obligatory on it?

First: If the loan was usurious, then you must repent to Allah Almighty.

Second: Zakat is obligatory on the money you possess if a year has passed over it. The differing opinions regarding deducting debt from it favor that you pay zakat on what you possess if you own an asset for investment that you can use to offset the debt, and you are not in need of it. Otherwise, there is no zakat due on you.

Third: The money you lent is part of your wealth, and zakat is obligatory on it. You can pay its zakat along with the money you have in hand, or after you collect it for the past years.