At the moment I'm finding they get out of sync reasonably frequently, and you get an error in orgzly saying 'Local and remote notebooks are different'.
My steps to resolve are:
- on desktop, copy `GTD.org` to `GTD.org.desktop`
- in orgzly, from the Notebooks view, choose to override remote notebook
- that means syncthing syncs `GTD.org` back on to the deskop
- then in Emacs, do an ediff of `GTD.org` and `GTD.org.desktop` and pick out the bits you want from each
- things will sync OK from there