Is it permissible for us to recover a sum of money that was deducted from our salaries due to a deficit in the pharmacy's trust, knowing that we are not the cause of this deficit, and in a way that does not reveal our taking anything from the pharmacy's trust?

It is not permissible to hold the employee or accountant at the pharmacy responsible for what was stolen from it if he fulfilled his duties and no negligence or dereliction of duty was proven against him, especially if he informed the owner of the pharmacy's need to increase the number of workers. If he is held responsible and deductions are made from his wages, he has the right to take his case to court. And if there is no Sharia court, then there is no harm in him taking his right without exceeding it, and this is the issue of al-Zafar (obtaining one's right).