Config are overwriting

When I ran tutor config save cms.env.json and lms.env.json are overwriting,

ie: I have updated some options in cms.env.json by manually editing. Then I have changed some changes to config.json. Then I got the message You should run “tutor config save” so I run that command Then cms.env.json and lms.env.json overwriting

Yes, this is normal. Please have a look at this section from the Tutor docs which explains how Tutor templates work: Concepts — Tutor documentation
In a nutshell: if you want to make your changes permanent, you will have to create a plugin: Plugins — Tutor documentation