How To Prevent Certain Folder To Be Overwritten During Plugin Update?

In a nutshell you cannot literally do this. For plugins and themes WordPress erases whole folder on update and unpacks full folder with new version in its place. You could emulate it by temporarily moving folder away and back, but that is inherently faulty solution.

Extension folders are essentially not meant to contain content in them. In more professional environments they very well might be locked down to read only and updates might be managed completely outside of WordPress (via version control or dependency management).

You can (and should) reliably write any content only to WP’s content folder.

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