Some folders empty on exFAT external HDD

[mrath]

For about 3 weeks now, I've had a problem with my Pi Openelec setup. I am using a WD external 1TB hdd as storage, formatted as exFAT, which has worked like a charm for a long time.
Even though the drive mounts like it should, and I can browse folders, some folders appear empty to OE. They are not empty, as I can list and play video files in these dirs when the HDD is plugged into my Mac. The problem is limited to recent seasons of currently running TV shows (i.e. folders that are added files to on a regular basis). However, transmission downloads fine to its download dir, and my movie dir is unaffected. In these TV show folders, no files appear anymore, not even files that were added before this error happened.
I have tried the following:

• Verify and Repair disk in OS X's Disk Utility - no errors
  
• Move entire affected folder (containing files) to another directory on the HDD (in OS X) - no effect, dir still appears empty on OE
  
• Move all files in affected dir to new dir (again created in OS X) - again, no effect
  
• Move single file out from affected dir - file is visible, but size appears to be 0B, and is unplayable
  

Here is the tail of dmesg, after connecting the HDD:

Code:

[ 9336.049796] usb 1-1.2.2.1: new high-speed USB device number 11 using dwc_otg
[ 9336.130986] usb 1-1.2.2.1: New USB device found, idVendor=1058, idProduct=1023
[ 9336.131025] usb 1-1.2.2.1: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[ 9336.131044] usb 1-1.2.2.1: Product: Elements 1023
[ 9336.131059] usb 1-1.2.2.1: Manufacturer: Western Digital
[ 9336.131074] usb 1-1.2.2.1: SerialNumber: XXXXXXXXXXXXXXXXXX
[ 9336.138302] usb-storage 1-1.2.2.1:1.0: USB Mass Storage device detected
[ 9336.149610] scsi5 : usb-storage 1-1.2.2.1:1.0
[ 9337.154185] scsi 5:0:0:0: Direct-Access WD Elements 1023 2005 PQ: 0 ANSI: 4
[ 9337.161485] sd 5:0:0:0: [sdb] 1953519616 512-byte logical blocks: (1.00 TB/931 GiB)
[ 9337.163764] sd 5:0:0:0: [sdb] Test WP failed, assume Write Enabled
[ 9337.166300] sd 5:0:0:0: [sdb] Asking for cache data failed
[ 9337.166343] sd 5:0:0:0: [sdb] Assuming drive cache: write through
[ 9337.194394] sdb: sdb1
[ 9337.200214] sd 5:0:0:0: [sdb] Attached SCSI disk

[mrath]

Well, tried some more testing, by simply moving files around in OS X and reattaching the HDD to my Pi. Tedious work.

It appears that some single files were corrupted in the affected folders, mostly .srt files. They showed up in OS X, but with zero file size, which is why I missed that in the first place.

After deleting all these corrupted files, the folders are now visible in OE, and thus to XBMC, again.

Marking as solved.