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

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

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

If "Verify Integrity" cannot repair places.sqlite, rename/remove all places.sqlite and favicons.sqlite files in the Firefox profile folder. Firefox will rebuild places.sqlite and restore the bookmarks from a 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 need to revisit a bookmark to restore its favicon.

See also:

• https://support.mozilla.org/en-US/kb/Bookmarks+not+saved#w_fix-the-bookmarks-file
• https://support.mozilla.org/en-US/kb/fix-bookmarks-and-history-will-not-be-functional

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

• Help -> 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

Thanks it seems like it worked (a couple favicons don't reappear even after I click them but that's not a biggie).

If Sync was involved you may need to do another "fix" if Sync continues causing a problem with your bookmarks.

If Sync was involved you may need to do another "fix" if Sync continues causing a problem with your bookmarks.

I don't use Sync (I said this in an earlier reply but it doesn't seem to appear for some reason.)