Hi
For those of you reading this post and still wondering how to correct this problem :
I installed fonpluz : nas-tweaks.net/40/installation-of-the-fonz-funplug-0-5-for-ch3snas-ch3mnas-dns-323-and-many-more/
activated ssh support : http://nas-tweaks.net/40/installation-of-the-fonz-funplug-0-5-for-ch3snas-ch3mnas-dns-323-and-many-more/#Activate_SSH
connected to my NAS : Terminal (OSX, Linux) or PuTTy (Windows) then "ssh root@MY_IP" without quotes of course and where MY_IP is your NAS IP eg 192.168.1.2.
Enter your password
Go to the shared folder which is causing the issue : "cd /mnt/HD/HD_a2/" for me which is the Volume_1 share of my NAS configured in RAID1
type "rm -R .AppleDB"
this will cause your NAS to rebuild its CNID database for the share.
do this for every problematic share
Problem solved, hopefully.