You must give write permission to the root directory of the machine where a version 3.5.2 file store is located to convert the file storage area during upgrade from version 3.5.2.
To grant directory permissions:
If you are running the WebSphere® Application Server instance by using the LocalSystem service log-on account and the file stores are located on the same server, then give SYSTEM write permission to the root directory.
If you are running the WebSphere Application Server instance by using the LocalSystem service log-on account, but WebSphere Application Server is remote from the file stores, then change the service log-on account from LocalSystem to an account that would be allowed write access to the file store directories.