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I had the need to use SSH to update the /etc/passwd, /etc/shadow, and /etc/group files in order to add multiple SFTP and SSH users for a single account, which is apparently not supported by cPanel. However, I'm concerned that cPanel might overwrite these when I make changes to other users in cPanel.

Does cPanel ever munge users that were edited outside of cPanel - that is, who are outside the knowledge of cPanel - by directly editing the passwd, shadow or group, or do cPanel user changes only affect the user that it is being changed?

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Yes, cPanel will modify those files. That's how it is able to create users and groups. However, I've added separate users, independent of cPanel, and cPanel never touched them. So, you should be fine. If you're concerned, just make a backup of those files, but I've never seen cPanel make any changes to a user which it doesn't know about.

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