If I decide to use "netupdate", and put all my leafbots configfile
on the hubs shell, will all the scripts I have added at the bottom
of my leafbots configfile dissapare when I ".netupdate -config"?
The config files from the hub's shell will overwrite the ones on the leaf bots' shells when you do a .netupdate -config. So if you edit a config directly on the leaf shell or FTP an updated config to a leaf shell, it will get overwritten.
The point of .netupdate -config is to be able to edit all the leaf bots' configs without having to login to each of their shells. Instead, you update the files on the hub's shell only, then do the .netupdate -config.