Put this code at the top of your scripts:
class A
end
class B < A
end
class C < A
end
class B < C
end
If you run the game, clearly you will get an error message indicating superclass mismatch for B.
Now insert the following script below
before the one above. Keep the two scripts separately, like so:

begin
for i in 1..1 # Yeah, just ignore this for now :P
code = $RGSS_SCRIPTS[i][3]
classes = code.scan(/class (.+?) < (.+?)/)
superclassCheck = {}
classes.each{|child, parent|
if superclassCheck[child].nil?
superclassCheck[child] = parent
elsif superclassCheck[child] != parent
p "Superclass mismatch! #{child} < #{parent}"
$RGSS_SCRIPTS[i][3].gsub!(/class #{child} < #{parent}/, "Object.send(:remove_const, :#{child})\r\n" + "class #{child} < #{parent}")
end
}
p $RGSS_SCRIPTS[i][3]
end
end
And if you run the game this time, it won't throw the error.