Unfortunately, this script does not preserve permissions and files will lose their executable state (script version 0.9, on Unix based systems). Fixed in 0.9.1
Version 0.9.1 is identical to 0.9.0 on http://www.vim.org/scripts/script.php?script_id=3641 . Script upload error?
Ooops. Guess I uploaded the wrong one. I fixed it. Sorry it took so long, I had no idea. This script appears to destroy symlinks on save, it will replace the link with a copy of the file it used to link to. Should at least warn about this on the script page.