If you use Sync, best is to disconnect Sync temporarily during troubleshooting.

This could be a problem with the places.sqlite and favicons.sqlite files in the Firefox profile folder.

• use the "Places Database" -> "Verify Integrity" button on the "Help -> More Troubleshooting Information" (about:support) page

If errors are reported with "Verify Integrity", close and restart Firefox or reboot and retry.

If "Verify Integrity" cannot repair places.sqlite, rename/remove all places.sqlite and favicons.sqlite files in the Firefox profile folder with Firefox closed. Firefox will rebuild places.sqlite and restore the bookmarks from the most recent JSON backup in the bookmarkbackups folder.

• keep a backup copy of places.sqlite in case a new places.sqlite database has to be created
• you lose the history when a new places.sqlite is created

You may have to restore an older bookmarks backup in the bookmarkbackups folder via the Bookmarks Manager (Library).

• Bookmarks -> Manage Bookmarks -> Import & Backup -> Restore
• https://support.mozilla.org/en-US/kb/restore-bookmarks-from-backup-or-move-them

See also:

• https://support.mozilla.org/en-US/kb/fix-bookmarks-and-history-will-not-be-functional
• https://support.mozilla.org/en-US/kb/cant-add-change-or-save-bookmarks

You can use the button on the "Help -> More Troubleshooting Information" (about:support) page to go to the current Firefox profile folder or use the about:profiles page (Root directory).

• Help -> More Troubleshooting Information -> Profile Folder/Directory:
  Windows: Open Folder; Linux: Open Directory; Mac: Show in Finder
• https://support.mozilla.org/en-US/kb/profiles-where-firefox-stores-user-data

Does it still happen in Troubleshoot Mode?

I didn't try it in troubleshoot mode. I followed the directions in the first response and verified the integrity of the database. That made all my bookmarks disappear so I had to restore them from a backup prior to the last upgrade and now everything works - except the bookmarks toolbar did not come back but that is not a major issue.

Check that the "Bookmarks Toolbar Items" control is on the Bookmarks Toolbar and that this toolbar is visible.

• https://support.mozilla.org/en-US/kb/customize-firefox-controls-buttons-and-toolbars

If "Bookmarks Toolbar Items" is not on the Bookmarks Toolbar, drag it back from the Customize palette to the Customize page to the Bookmarks Toolbar If missing items are in the Customize palette, drag them back from the Customize page to the toolbar If you do not see an item on a toolbar and in the Customize palette, click Restore Defaults in the Customize palette window to restore the default toolbar set.