External disk file loss

My media files are on an external harddisk, a WD myPassport, 4 TB. It's partitioned with GPT as one big partition, formatted ExFat. It's USB powered, which is why I use a powered hub. It gets mounted at boot and spins down when I shutdown.

Lately I noticed files missing from a recently accessed folder. Today I witnessed the same, almost in real time. I was playing a test file, adjusting audio offset. I stopped playing the file, edited advancedsettings.xml, then rebooted the box. Entering the same folder with the test files it was empty.
Powered down, attached the disk to my mac, two out of four files in the folder where missing. "Repaired" the partition with OSX' disk utility, which found errors in the directory structure and claimed to have fixed it. The two files are still gone.
After that repair LE was also able to see the remaining files.
The last time a whole folder went missing.

I used testdisk (before disk utility) but the partition layout seemed to be ok. Contrary to LE (no files) and OSX (2 files out of 4) testdisk showed all four files (and not as deleted). So I could copy them. I would however not "write" the found partition table, as it contained a lot of strange files in various places as well.

So 1st, I think that something is definitely wrong with the disk.
2nd but neither disk utility nor WD's tool can find anything wrong with it (now).

Do you have any ideas what could have gone wrong? I mean, LE shouldn't even have had to write to the disk, it was just reading the file from there? Still, the files went missing by rebooting.

Any tests or logs I can provide to narrow this down?

Thank you

It happened again.
Do you know if this is something that might result from LE's exfat implementation?
I have now reformatted the disk and am in the process of copying all files back to it (that will take some time). I hope there was something wrong with the FS that isn't anymore, but I'll see if it happens again.
Sadly I have not found a viable alternative to exfat for my purposes.
Any ideas to troubleshoot are still welcome.

Quote from lrusak

You can always try running fsck.exfat on the Disk to see if there are errors.

thanks for the suggestion!

this is what disk utility on OSX does when repairing, it fires fsck.exfat from the GUI.
do you think I might get different results if I run it from LE?

also note that as described in the OP, OSX was able to see two files while LE saw none before fsck, afterwards both saw the same, but two files still were missing. in the other instance fsck didn't bring back any files.

WD drive utilities didn't find a fault with the disk on a "full disk test", which claims to search the whole disk for bad sectors.
In the meantime I found the software "Scannerz" which supposedly finds hard disk faults that other software doesn't, but I am hesitant to pay for it since the disk had no problems during the last year while using it on OSX and exhibited the mentioned problems soon after I started using it with LE, which leads me to suspect software instead of hardware problems as the underlying cause.

The only other thing that changed is that the disk is now attached to a powered hub because it is common knowledge in Kodi/LE forums that bus-powered disks can't get enough juice for reliable operation from an ARM device. Do you think that the hub could lead to the described symptoms?

I have used the disk twice since reformatting and so far no visible issues, but there are a lot of files and folders on this disk so I can't be sure whether or not it is fixed. Still hope for some suggestions or clues as to why this might have happened in the first place.