No, it won't hurt your careers at all. Just make sure you wait until you are in port between patrols.
The Rollback simply disables all the settings so the new mod doesn't interfere with what's already there (at least I think that's how it works). Then the next time you use Commander it reads everything that's there and re-enables everything together, including the new stuff.
Unless you are a dedicated mod maker who uses Commander for testing there is no reason not to use 'Auto-Rollback'. That way you never need worry about it again. That's what I do, and I've never had a problem.
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“Never do anything you can't take back.”
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