Jia-Mei, first of all, if you are running that "Server deletePropertyValue" command from within the subshell. You'll need to restart the subshell after copying the XML file to the .../br/xml/cli directory.
There is no direct method in Java to stop characters from echoing to the screen when running from a console. The standard method for doing this across all dos/linux-based Java apps is to refresh the line constantly. This is what you are seeing.
I have looked for ways to do this myself in Java and have found, throughout google, only this approach. As a work-around, consider using the user_info.dat file to authenticate with the server when you use the blcli or blcli subshell.
We are planning on fixing the password issue in the 6.3.2 release.