Is it possible to recover files owned by a non existing owner?

I am trying to get backup so that I can upgrade my system to latest version of Ubuntu. Now while copying files some files I found are owned by user #1000 so i could not take backup of those files.

This suggests that such user does not exist in my system.

So is there a way to take backup of those files?

Note: I am using a live cd to take backups.

In unix, the owner of a file corresponds to a numeric user id. Just because the numeric user ID shows up instead of a username does not mean that the user does not exist, and really doesn't matter even if that is the case. (There are multiple possible causes of this, including the user not existing on the system.)

Backing up files owned by a non-existing user should not be any different than any other file. Possibly you are running the backup software as a different user that doesn't have read access to those files? Typically backup software would be run as root rather than a regular user exactly to bypass this issue.

If you are running the backup as root, is it possible this is only a warning, and the files actually did get backed up? Backup software might try to store the username of the file owner in the backup, so that if files are restored on a different system or after users are recreated with different user id's, the ownership is mapped to the correct username. Failure to look up the user might generate a warning.

User 1000 is typically the first user on the system. Did you possibly delete that user after creating another user?

If you are using a live cd, did you use sudo to escalate to root before running the backups?