I'm doing an rsync backup of my home directory on my web host. My webhost uses cpanel and I noticed that there are some cpanel directories in my home directory that I'm backing up. Is this going to cause issues if I ever do a restore? Will it revert my cpanel changes to that date as well? or will it just cause more issues than I want to deal with?

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Just exclude the .cpanel directories with rsync and you should be fine.

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