Dear @widtmann,
Thank you for posting your solution!
I noticed that files could disappear from FlashDisk if they were written not long before coldboot (iMX6 WEC7 BSP1.6). I spent a week fighting with disappearing, trying different delays, sending IOCTL_DISK_FLUSH_CACHE, executing preparefs etc. Like in your case, when batch copying was performed, the same file disappeared, it was totally reproducible.
With disabling the TRIM function, the problem has gone.