Let me explain something about fun_plug - it's a script, a list of commands that the DNS-323 looks for when it starts up, and if it finds the list, it executes the commands, whatever those commands are.
What fun_plug does and how it does it depends on what commands are in the list - that means that my fun_plug may not do the same thing that your fun_plug does - I can upgrade the firmware and not worry about the effect it has on my fun_plug, because I know what my fun_plug does - I created it. I can't tell you what the effect on your fun_plug will be, because I have no idea what your fun_plug does - if you created your own fun_plug, then you get to answer that question yourself, if not, then you have to ask whoever created the fun_plug you're using.
Are you going to lose configuration changes - that may depend on where they are stored - you can use fun_plug to overwrite the stored configuration and if that's what was done, then yes, you'll lose them, on the other hand you can also store those changes on the disk and have fun_plug apply those changes every time the unit starts up, and if that's how it was done, then no you won't lose them.