Bookmarks get mixed up during sync.
Each time Firefox Sync syncs my data, all the bookmarks in my Bookmarks Toolbar, which are within separate folders, get mixed up. All bookmarks in separate folders are all in ONE folder, the other folders then are empty + the position of the folders are mixed up as well.
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We regularly see reports that using Sync with desktop and mobile devices can cause the bookmarks to get corrupted.
You can try to disconnect all devices and change the password of the Sync account to reset data on the Sync server.
You can check for problems with the places.sqlite and favicons.sqlite files in the Firefox profile folder.
- use "Verify Integrity" button on the "Help -> Troubleshooting Information" (about:support) page
In case errors are reported with "Verify Integrity" close and restart Firefox and retry.
If necessary you can restore the bookmarks from a recent JSON backup.
Best is to reconnect one device at the time and wait for the initial Sync to finish before connecting another device once you have fixed the bookmarks.