Has iCloud and/or Safari just borked your bookmarks? This happened to me yesterday. Here’s how I fixed it…
Bookmarks.plist in Home > Library > Safari.The crucial thing is to avoid at all costs selecting Merge when you re-enable bookmark syncing on the iDevice(s). This is what causes problems—and I re-ran the scenario several times to confirm this. Apple, please add an Overwrite Data on the Device option here. The choices should not be solely Merge and Cancel.