The first step is for us to understand what “missing” means? Have you got any mechanism (U-Boot, SD card boot, etc.) that will allow you to mount and look at the contents of the NAND file system?
If you look at the /bin directory (ls -la /bin/busy*) what do you see? Have the files been deleted? Truncated? Zero length?
What file system are you using on the NAND flash? How are the devices being reset during the various boot cycles? If it is a hardware reset then some file systems are less resilient to it than others but I would expect in that case more fundamental boot issues.