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If you just want to edit the registered environments you created while using configure script, just edit the environments.properties file.
You can find this file in same directory of the repository that you created for the registered environment.
To delete, you can simply delete that directory - which is the repository for the registered environment.
Also, to point the configure tool to another repository, edit the .configure file. You can find this file in <APPIANHOME>/_admin/_scripts/configure directory. For example, mine looks like this:
#Mon Oct 03 17:12:40 IST 2016jboss.path=F\:\\jboss-eap-6.4.0_for_163repository.path=F\:\\Appian163_config_repo
I can change these values and the tool will pick it.
Hope this helps.