Git plugin calls fetch with branch always with deleteBranchIfExists, which in case of CliGit results in the call of

launchCommand("checkout", "-f", ref);

which in turn throws away all local modifications and leaves a clean status.

in JGit, setForce() is also used, but does not seem to work as expected. There are already comments in the code discussing this behviour, but they only point to checkout conflicts.