Unrelated to the glitch at hand, but would it be worth the effort to have a quick toggle for the autosync bookmark option somewhere to avoid digging through the preferences for it? I was thinking a "toggle autosync [off/on]" in the menu.
Two reasons I can see the usefulness of this:
1. Needing to restore the bookmark from Calibre without the incorrect bookmark syncing in first.
2. Not cluttering up an unrelated debug log with Kobo Utilities checking a few hundred books for bookmarks.