I have a jury-rigged system, as I use my 2-in-1 stylus-equipped Chromebook for most of my reading and annotating. It's not very elegant, or FOSSy, but it works reasonably well.

I basically use Dropbox as a back-end, using Autosync for Dropbox (fka Dropsync) [0] on Android and ChromeOS (and the vanilla Dropbox Linux desktop client on Kubuntu) to keep the files synchronized (storing them on SD cards on my phone and Chromebook). I have it automatically sync frequently, and the app automatically uploads local changes to the cloud.

For PDFs, syncing the highlights is of course trivial; as a reader, I use Okular on Linux and Xodo [1] on Android/ChromeOS. Xodo has more features -- I like using my Chromebook's stylus to scribble notes in the margins -- and everything ports well to Okular, and vice versa.

For EPUBs, I use Calibre on Linux and Moon+ Reader Pro [2] on Android / ChromeOS. In practice, though, I use the latter almost exclusively; it has a built-in Dropbox sync functionality [3], though I'm not sure the highlights etc. are accessible by other apps.

[0] https://metactrl.com/

[1] https://www.xodo.com/

[2] https://moondownload.com/download.html

[3] https://raymondlamsk.blogspot.com/2018/03/moon-reader-how-to....