These issues are why I gave up syncing more than a decade ago (with Kindles, then). It was just faster and less annoying to find my place purely by memory. And I don't have a particularly good memory by any yardstick.
It's indeed sad to read that nothing has improved in more than 10 years and sync problems are still going on. Makes me less than hopeful that if Kobo eventually implemented syncing for sideloaded books, it would then work correctly.
