Erin, I have also experienced this recently on version 2.4. In our case, 5 students show as submitted with a time stamp, but there are no files attached. The instructor actually retrieved the files, graded, and left feedback before the attachments/submissions disappeared.
I tracked down the assignment submissions in MySQL and the files show up, but are nowhere in our files. The only related issues have been years ago with 1.9. I hope we can find a solution soon.