Matlab issues the message that you refer to in "Change folder is the option that sometimes matlab ask before running the script" when the script in question is not on the search path or the current directory. See Search Path View and change MATLAB search path and What Is the MATLAB Search Path?
Change folder vs change directory
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What is the difference between chage folder and change directory?
Change folder is the option that sometimes matlab ask before running the script and change directory is a matlab command:cd.
My question is about their applications and differences.
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