Where do you see this second set of bookmarks ? Do you see it in the Bookmarks Manager (Library) or sidebar (Ctrl+B) ?

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.

I click on ‘Bookmarks’, start my Bookmarks list to scroll through until it reaches the end of the first set and then I see an entry that has the Internet symbol and ‘Get Bookmark Add-Ons’ beside it and then the previous list is repeated.

I ran the 'Verify Integrity' and, as far as I know, it ran OK. I still wish to know if removing the second set of Bookmarks will hurt. I will make sure to back up the Bookmarks before I do that.