I would recommend making a good backup of your data. Because you're using Windows 98SE, you're using the FAT32 filesystem, which has a bad habit of - every now and then - corrupting the file table, resulting in data loss.
If you can, I'd recommend reformatting - it will wipe the disk and create new file tables, effectively fixing the problem. I don't believe there's a way to repair partially corrupted/damaged file tables - but someone may know of software to do that.
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