Generally, this does not happen.
Well, it did happen - on a live site, after following your documentation.
The update from Wayne Corp 2.0 to 2.2 broke the site, and once I fixed that by selecting a preset, all the Custom Code (CSS, JS, head/body code) was gone. I now have no option but to restore a full backup.
I’ll restore from backup, but “check with your hosting for restoring a backup” isn't an acceptable answer.
An update to your template has deleted my customisations. I’d expect you to treat this as a bug, try to reproduce it, and confirm whether this is a known issue and something you plan to fix or warn other users about.