Restore a Deleted Favorites File

Restore your Safari bookmarks and reading list

• Go to Settings on iCloud.com, then click Restore Bookmarks (in the Advanced section).
• Available versions are listed by the date and time they were archived.
• To the right of the version you want to restore, click Restore.
• There may be more versions than can be shown at once. Scroll to see more.
• Note: Wait until iCloud finishes restoring your Safari bookmarks and reading list before you change them. While they’re being restored, any changes you make aren’t saved.

  https://help.apple.com/icloud/#/mme6182cfc37

If you have a Time Machine backup, go to a backup where you had the Bookmarks and paste the below into the search box. Restore that file and see if it works.

~/Library/Safari/Bookmarks.plist.

I'm not understanding what you are seeing. Do you see the Bookmarks.plist?