I suffer from the same issue. I use KOReader, which does do sync, but uses its own zsync protocol, which basically nothing else supports.

I use Kybook 2 on my iPad. I think Calibre supports syncing with Kybook 3, so you could try that.

If you really want highlight syncing etc, it might be worth migrating to a Kindle-first workflow? But PDFs aren't there.

Why is this so hard :( Why can't everything use a standard progress sync protocol? (KOReader's is at https://github.com/koreader/koreader-sync-server)