Is it permissible to waive financial entitlements from clients who were introduced to the company as compensation for sums of money withdrawn from the company's custody without repayment, in the event of not knowing the total amount withdrawn and being unable to repay?

The money you possess is a trust that must be safeguarded and returned to its rightful owners. It is impermissible to transgress against it, as that constitutes a betrayal of trust, and Allah has forbidden betrayal. You must repent to Allah by returning the money taken from the company. If the exact amount is unknown, you must return what is most likely sufficient to cover it. If you have a right against the company that is sufficient for this purpose, then it is permissible to waive that right in exchange for what is owed. Otherwise, the remainder must be paid. If you do not have the money readily available, then you are liable for the debt until it is paid.