If your mother's pension application file has been lost by the concerned office, several legal steps can be taken. Firstly, consider using the Right to Information (RTI) Act to obtain details of family members listed in your father's service records. It's also advisable to send a formal reminder letter for the pension sanction along with a fresh set of papers. If these actions don't yield results, consult a local lawyer to serve a legal notice and potentially file a case in the relevant Tribunal or High Court for adjudication.