Can you confirm whether the file itself is being deleted or the ssh keys inside the file get removed?
If the file itself is being deleted, you can check your startup script which might help you to find the reason behind it.
On the other hand, the file ~/.ssh/authorized_keys is updated with every modification in SSH key metadata values. You can refer to this article for adding and removing SSH keys. Also, you can use the add-metadata command in Gcloud as another option.
If you suspect that the SSH keys are being deleted in your project, kindly provide the content of /var/log/syslog file to take a closer look at it.