Because you mentioned diskless booting, we assume you are talking about
installing Apple IIGS/OS 5.0 on the Macintosh AppleShare File Server.
The only copies of BASIC.SYSTEM and BASIC.LAUNCHER that are installed by the
Server Network Startup script are those installed at the root directory. The
copy of BASIC.SYSTEM in the Macintosh System Folder is installed by the Apple
II Setup installer when the server is set up for use by Apple IIs. A copy is
put in the System Folder so that the server will have a default startup
application for all Apple II users.
It is perfectly acceptable to remove the copy of BASIC.SYSTEM in the System
Folder, so long as you remember to set a startup application for each Apple II
user. You should not remove those copies of BASIC.SYSTEM and BASIC.LAUNCHER
located at the root directory unless there is no need for Applesoft BASIC.