Hello Shezza. Welcome to the club. I spent man hours with similar issues but mainly with loosing my Regits which I went through great pains to create. Response form this forum has taught me a few things that I am going to share with you.
1. Once you select the USB you are going to use, BEST to format on the Keyboard, forget using the computer because if using a high speed 3.0 USB, you can not get the keyboard to read the exfat format 100% of the time. Has to be formatted in the slower FATS speed.
2. Once you load your USB and start using it on the keyboard do not re-organize/move things around on that same usb as the REGITs keep track of the directory paths of the Syles, PADS, Voices, etc. I did this a few times until it was pointed out to me. Now I just append or insert but not reshuffle any new incoming files.
3. On my Windows 10 I encountered the same issue as you, and my formats sometimes took hours on the pc after an attempt of a copy from keyboard loaded usb or usb to pc failed. All because of the format type. If you use your USBs primarily for PC only I found no issues at all.
So format the target USB on your keyboard, then copy your source to the target and you should be fine on the copy part of things. I can not say that this will address you missing files and that they will be recovered. Keep in mind that if your source USB is in exfat format, just bite the bullet like I did and start over. I am glad I did as painful as it was. Check this thread out.
https://www.psrtutorial.com/forum/index.php/topic,58314.msg452080.html#msg452080 Hope this helps... Regards! dom