This is a tricky question. I suspect it will require some advanced knowledge of file systems to answer.
I have a WPF application, \"App1,\" targeting .NET framework
I had a similar problem and I was able to trace my problem to corrupted HDD.
Description of my problem (all related informations):
Disk attached to mainboard (SATA):
SSD (system),
3 * HDD.
One of the HDD's had a bad blocks and there were even problems reading the disk structure (directories and file listing).
Operation system: Windows 7 x64
file system (on all disks): NTFS
When the system tried to read or write to the corrupted disk (user request or automatic scan or any other reason) and the attempt failed, all write operations (to other disk's) were incorrect. The files created on system disk (mostly configuration files by another applications) were written and were valid (probably because the files were cashed in RAM) on direct check of file content.
Unfortunately, after a restart, all the files (written after the failed write/read access on corrupted drive) had the correct size, but the content of the files was 'zero byte' (exactly like in your case).
Try rule out hardware related problems. You can try to check 'copy' the file (after a change) to a different machine (upload to web/ftp). Or try to save specific content to a fixed file. When the check file on different will be correct, or when the fixed content file will be 'empty', the reason is probably on local machine. Try to change HW components, or reinstall the system.