Starting around 4 months ago I started to notice that when I update FF I lose some bookmarks but if I uninstall and reinstall then I get them back so I did a Google search and it sounds like it might be an issue with my places.sqlite file so should I try use Places Maintenance?: https://addons.mozilla.org/en-US/firefox/addon/places-maintenance/
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You can check for problems with the places.sqlite database file in the Firefox Profile Folder.
So how do I use Places Maintenance? I just installed it and cant figure it out.
The Places Maintenance extension may not fix this issue as it only works in very rare cases to clean up the database.
Most of the time the only thing that helps is to delete the places.sqlite database file and let Firefox create a new file.
You should be able to run the extension via the Options button on the "Tools > Add-ons > Extensions" (about:addons) page.
OK thanks so could duplicate folders cause this to happen? Lets say the unsorted bookmarks folder for example.
The real unsorted bookmarks folder should have a special folder icon.
If there are duplicate folders then that can possibly normal folder that can be deleted via the right-click context menu.
This can happen if you import a HTML file.
If the folder is a real duplicate then best is to delete the places.sqlite file to force Firefox to rebuild the bookmarks from a JSON backup in the bookmarkbackups folder.