Executable binary used to run, now does nothing

I have a C++ program I've compiled and have tested and know works. The compiled program is called by a startup script and has been consistently working and showing output as expected. Somehow the executable has stopped working on startup. Even worse, when I try running the binary outside of the startup script it now finishes instantly with no output (it's a long program with lots of console messages even on failures).

This has now happened three times in the last week. Recompiling the program fixes this issue, but I don't want to have to do this multiple times per week. Any ideas on what's happening or how to fix it? (This is on an Intel Edison with Debian)

EDIT: I'm not sure if this matters, but this program will always be running when power is cycled, but not at a predictable state. Unfortunately, it won't be in an environment where I can do proper shutdowns. Power will be cut abruptly. Because the executable is not being edited while power is cycled I'm not sure how it would break that file.

EDIT: Here's how I start things in my script: (cd /root; bin/prog &; disown)

prog runs until power is interrupted