When you say retry, did you completely restart the installation process, or did you just go back to the installer screen and retry the step that does the backup?
If you retried the step, you should still have all the logs of the installer on the updated host in /var/log/installer/ in that case, I would suggest checking the dmesg-log, that sounds like a disk error to me.
Having removed the file would not impact the newly upgraded host in anyway, it just means you lack that file in the backup, so that could have an impact in case you were to restore, which I hope you won't need.
Other than that, I would encourage you to check your disk health as this could be a sign of hardware error.