Is it permissible to deduct a sum of money equivalent to the Eidiyyah that was not disbursed, considering it an unspent salary increase, in order to settle an outstanding debt?

As long as the employee who took the Eidiyah amount is not the owner of the pharmacy or the place, the discount will be from the money of the owner of the place or the pharmacy. As for his request for a salary increase, he should direct this request to the owner of the place or his agent. If they agree on the increase, then that is good and blessed; otherwise, he has no right to an increase without agreement and a contract.