Without even knowing what sort of files you are talking about that's impossible to answer. Though a simple reboot certainly shouldn't remove any files.

Just to be sure, where were you storing these files: on the device or on removable storage? Were any synced with any cloud service (check, there may be cloud services enabled by default)? And if they are stored on a removable card, is it a new one and are you certain it is what it's supposed to be (there are a lot of fakes out there)?

I don't have an answer, those are just a few things that come to mind.