The links were probably deleted along with the rest of the old Mozilla folder when you upgraded Mozilla. Next time, before you upgrade Mozilla, export your bookmarks to a safe place. Just go to the Bookmarks menu, click Manage Bookmarks..., go to the Tools menu, and go to Export...
Then after you've upgraded, import the backed up bookmarks from the same menu.
If you're referring to your toolbar being missing, just go to the View menu, go to Show/Hide, and check Personal Toolbar.
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