You cannot modify the config file once a chain is up and running, i.e. once multichaind is called for that chain, since the configuration is baked into the immutable blockchain itself.
May I recommend following the instructions on this page:
If you want to reuse a chain name that you used previously, make sure that multichaind is not currently running for that chain, and then remove the corresponding directory which will be: ~/.multichain/[chain-name]
You should then be able to start again with a clean slate.