Need to ask you sone questions:
1. What exact Mac model do you have?
2. What exact Mac OS are you using?
3. Have you ever done an disk cleanup/maintenance/repairs, from a software perspective? By that I mean have you ever run any disk-related software to help with those tasks? There are some excellent products available (both free and commercial) that can help you with that.
4. This is critical: are you making backups to an external device? If yo are, what software are you using for that?
5. Any idea what type of file it was?