You need to delete the variable from the plugin file. This plugin will reproduce the problem:
<?xml version="1.0" encoding="iso-8859-1"?>
<!DOCTYPE muclient>
<!-- Saved on Tuesday, December 06, 2005, 11:15 AM -->
<!-- MuClient version 3.71 -->
<!-- Plugin "variabletest" generated by Plugin Wizard -->
<muclient>
<plugin
name="variabletest"
author="Nick Gammon"
id="d2be8865570f7729bd130584"
language="Lua"
purpose="tests a problem Gore has"
save_state="y"
date_written="2005-12-06 11:14:46"
requires="3.60"
version="1.0"
>
</plugin>
<!-- Aliases -->
<aliases>
<alias
match="target *"
enabled="y"
variable="victim"
send_to="9"
sequence="100"
>
<send>%1</send>
</alias>
</aliases>
<!-- Variables -->
<variables>
<variable name="victim">Gore</variable>
</variables>
</muclient>
Note how variable "victim" is declared in the plugin itself as Gore? Now if the plugin changes that, in this case you could do it by typing "target Nick", then it now has "Gore" in the plugin file, and "Nick" in the state file. Then you get the warning about overwriting a variable.
Basically variables that might change should not be declared in the main plugin file.