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Config file will not overwrite

I'm saving elements of an array into a config file by chaning the key name "(input) (1)" etc. When I overwrite a file with less elements than were originally in the file, i do not overwrite the whole file, only the beginning up to where the file should end. (old data remains). So how can i get it to overwrite the file and not just data in the file?
 
 
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This is by design of the configuration file functions. All you're asking it to do is to replace keys. In order to do what you want you would need to first remove the section where you're writing the keys. There's a function in the config file VI palette to do this.
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