This is unavoidable 
When you reboot the FXT, you also restart its USB stack - which will be seen by Windows as if the FXT were unplugged, and then reconnected.
If you want your C# application to survive this, then you will have to handle the Windows System events which indicate that the USB device has been removed & (re-)inserted.
See: avrfreaks.net/comment/154900 … nt-1549001
And: avrfreaks.net/comment/154902 … nt-1549021