It's a bit of a pain, but you can store `~/.local/share/okular/docdata/` in version control or your favourite cloud storage provider, and then you'll get synchronised annotations.
When I say a bit of a pain, I mean it - I switched to Mendeley with great sadness because its mobile application means I can read and annotate papers on my tablet and have it synchronised perfectly with my desktop.
On a semi-related note: the Mendeley mobile application makes selecting text a joy on a touchscreen with a kind of magnifying glass. I really wish it was built into Android system wide.