Hello! I haven't tried it myself, but I am 100% sure it will not remove the contents of your website. Backing up is a safety option: if you keep you back-up file updated regularly (as in: when you make changes to your tree on your website, download a new version of the gedcom file and eventually overwrite the old one), should anything happen to your website here, you can always re-upload it (and, in theory, upload it to another platform should you choose to, or open it in an offline software). Your website won't be affected by backing up.
All the best!