SSH – How to Transfer Files

If you're using Bash, you can run disown -h job

disown

disown [-ar] [-h] [jobspec ...]

Without options, each jobspec is removed from the table of active jobs. If the -h option is given, the job is not removed from the table, but is marked so that SIGHUP is not sent to the job if the shell receives a SIGHUP. If jobspec is not present, and neither the -a nor -r option is supplied, the current job is used. If no jobspec is supplied, the -a option means to remove or mark all jobs; the -r option without a jobspec argument restricts operation to running jobs.

I would use rsync as it means that if it is interrupted for any reason, then you can restart it easily with very little cost. And being rsync, it can even restart part way through a large file. As others mention, it can exclude files easily. The simplest way to preserve most things is to use the -a flag – ‘archive.’ So:

rsync -a source dest

Although UID/GID and symlinks are preserved by -a (see -lpgo), your question implies you might want a full copy of the filesystem information; and -a doesn't include hard-links, extended attributes, or ACLs (on Linux) or the above nor resource forks (on OS X.) Thus, for a robust copy of a filesystem, you'll need to include those flags:

rsync -aHAX source dest # Linux
rsync -aHE source dest  # OS X

The default cp will start again, though the -u flag will "copy only when the SOURCE file is newer than the destination file or when the destination file is missing". And the -a (archive) flag will be recursive, not recopy files if you have to restart and preserve permissions. So:

cp -au source dest