You can rebase from the latest revision in the upstream branch, but you can also do safer rebase by choosing the permalink. For example, if you specify "last stable", then Jenkins will look for the last stable build, then rebase with the corresponding Subversion revision. Thus you know that you are rebasing to the known good state.
If you don't want Jenkins to automatically rebase, you can still use the "Rebase From Upstream" link from the left to manually initiate the rebase.