I don’t know if this question can be answered by an outsider, but I would start with any logs you may have for the site. Logs can tell a story and nothing happens without a reason. Also, those two events may or may not be related.
Since we don’t have any data to base our answer on, we can only guess. If I had to guess, the header might have disappeared after a plugin, theme, or WordPress update. The backups might have disappeared because you either exceeded your space limit, someone accidentally or purposely deleted them, or they were purged because of a violation in the terms of service with GoDaddy.
Regarding the last point, if this is a shared hosting account, I remember back in the day one could not use a shared host as a data dump, i.e. upload a bunch of files that aren’t being served externally to visitors, which backups aren’t. On top of that, if GoDaddy offers an actual backup service, they may not want you to use your own on-site backup service for free, hence the terms of service violation. I could be completely wrong on this, but that’s what comes to mind based on the information I have.
Your best bet would be to reach out to GoDaddy, considering actual files have disappeared on the server, and ask them if they have any insight into what might have happened.