Wait until Jenkins/Hudson is idle to perform a backup (recommended/default setting). However, you can do a backup without waiting for the idle condition. This may cause problems which results in corrupt backups, because files that will be written in the same moment as they will be backuped could be locked in the file system. Nevertheless, in the case of long running jobs (e.g. test jobs) you probably do not have a free time slot for your backup task. During this jobs you are sure nothing is changed or locked in the file system (e.g. because the build job is done on a slave). In this case you could disable this option to perform a backup in parallel to a running job.

NOTE:
We cannot 100% guarantee that the backup is correct if you disable this option.