Resolution:
When reconfiguring a Manager from a directory that is a symbolic link, its files will get overwritten.� For example, if you installed a GridServer Manager in /manager, then made /sym-manager a symbolic link to /manager and initially configured the Manager from /sym-manager, later attempts to reconfigure it from /manager would fail.

You should not install or run the GridServer Manager from a symbolic link. Attempts to later reconfigure the Manager will result in files being overwritten, as the Manager will think both directorys are different and copy the files from one directory to another, essentially deleting the files. To ensure that this does not happen, only run the Manager from a non-symlinked directory.