Refusing to return a security cheque after securing the loan with another

I issued a security cheque to my company owner for another employee loan who did not have a bank account at that time.

Now, the same employee has a bank account and a cheque book and he has issued cheque against his loan to the company, to which I issued cheque before.

At the back of both cheques (Issued by me and another employee) mentioned that cheques are only for security purpose against the employee loan.

My owner is refusing to return back my cheque. What should I do?

She is now holding 2 security deposit cheques against 1 single amount of loan.