In addition to what biketool said, I can attest that I had numerous reboots caused by one file manager or another. Copying a large file is almost a certain killer. It does not matter where you copy it, SD or internal storage. The reason is that the OS does not go idle often enough during a long file operation and the watchdog kicks in and reboots the phone. It is definitely the application's fault: I reproduced it myself in my own application that I was developing. The stock File Manager does not suffer that problem.

An unexpected reboot can cause a serious havoc with the file system. Especially if the reboot took place during a file system operation. A corrupt file system can cause exactly the sort of symptoms you describe.

If you use BackupMenu, I recommend using it ASAP to export all your partitions and check them all on a big PC. Even better, if you have a recent backup, just save yourself a lot of trouble and reflash the system, then restore from the backup.