1. I have the mount_shares_locally script running on my box, but I don't remember if this script was running when I had the problems. ( I don't remember if I started using this script before I updated greyhole or after).Awesome. Were you running the mount_shares_locally script when these problems occurred? Did you do these rename/moves from the HDA or using a client?
2. I am doing the renames/moves from the windows 7 client. This happens almost daily: every time I download a file it goes into a gh share, and I then rename it and move it into another folder in the same share or in another share (I think the problem happened when I moved into another folder in the same share, but I'm not sure).
With the old amahi version it seems that if I renamed the file and moved it too quickly (perhaps if I renamed the file 2 times, I'm not sure) the link would still be there, but the file would be lost. This happened several times. I lost about 50 Gb of data until I update greyhole. And since I updated gh this problem never happened again.