I was bulk renaming files from windows file explorer through samba on a raspberry pi 4 (LE 11.0.1), on a usb portable drive formatted ntfs. I've seen that some files are simply dissapear from the explorer, and not just the ones renamed.
With a two day work on this problem, I checked if the problem is not on my windows computer, set different versions of samba protocol, change power supply of the raspberry pi, installed different versions of LE, use different usb drives or sata with usb adapter, even try with the same drive connected to a router that have samba sharing, and finally formatted the usb drive to ext4.
What I can say, is that with LE 10.95.0 and above, the problem can be reproduced. I read above at mglae that LE11 changed the ntfs driver from user space ntfs-3g to in kernel ntfs3. For sure there is something wrong there.
The problem is not samba, because renaming of the files by ssh-ing the Rpi give the same problem, neither the drive or usb, because with the same drive formatted ext4 the problem disappear. Looks like some cache of the file names in the folder, not commited at the right time.
The drives seems to be "recoverable" by chkdsk /f, it said something on step 3 that some files are not indexed and will be reconnected with the folder that belongs.
I advise those that said they have no problems, to try to rename 20-30 files in a folder on a session and you might find this issue. If you just play the files from the drive you'll have no problem, I'm not sure that when writing files you can lose data, but for sure when renaming there is a big problem.