I don't think the Home settings will affect what appears in the bookmarks toolbar, though they do include an option to show some of the bookmarks on your home page and/or new tab.
From what you say, Roobarb, it seems that the bookmarks and/or containing folders have mysteriously disappeared from the Bookmarks Toolbar folder. I don't know why or how this might have happened, but I have two suggestions for getting them back. Before you try either of them, though, go to the Library and select All Bookmarks on the left. Then in the top menu use the Import and Backup item to create a backup (onto the desktop will be fine - it's a temporary measure in case my suggestions don't work and you need to get back to where you are now).
First suggestion: in the same Import and Backup menu, hover on Restore. This should bring up a list of backups which Firefox has done automatically, and with any luck one of them will get your toolbar back to how it used to be, though you'll lose any bookmarks you've added since the date of the backup. (Use the same menu ('Choose File' at the bottom) if you need to restore the backup you created manually.)
Second suggestion: if the bookmarks/folders you want are in the Library but not in the bookmarks toolbar, when you're in the Library you can right-click and copy them and paste them into the toolbar folder. (Moving or dragging is also possible, but I'm suggesting Copy just in case there's a problem I don't understand with the toolbar - this way you'll still have the bookmarks/folders in the location you're copying from.)
Just one more thing - have you updated Firefox recently, or added or updated any extensions? I found a very old support forum post where someone had what seemed a similar problem, and an updated extension seemed to be the culprit.