Share your experience!
I am leaning towards an issue with the card but it is odd that it is the same files deleting each time, have you tried using MediaGo to transfer the files to the phone?
Could you try two things?
1. Try another (even small 2 - 8 GB) SD card, put those disappearing files in the same folder and give it a try.
2. Backup data and format entire SD card from phone, then load music through USB cable.
If in 1 & 2 files disappear I would suspect that you have some kind of malware on the phone.
If disappear only in 2 probably SD card is broken and you need to replace it.
Uninstall that app if possible and try for longer time.
What is the pourpose of this app? Maybe it treats your files as garbage?
Troubleshooting to fix SD card deleting the files by itself:
Once, the process gets complete, you can then add files on your SD card and again repeat the CMD process. Now check the files on your SD card.
If files are still available on your card it means your problem is solved. You can then eject SD card safely from your computer and insert it back your phone.
Hopefully, your files from SD card now will not get deleted by themselves.