Sorry for the fuss, it's already resolved!
After checking the internal Bookmarks files "Bookmarks" & "Bookmarks.bak" located in "C:\Users%User%\AppData\Roaming\Opera Software\Opera GX Stable" I verified that my bookmarks were still there, like this What had happened was that when I synchronized again, for some reason the old ones that I deleted were added, and what I already had was moved to the end of everything, and since I had many in front of me I couldn't see them! 
So now you know what to do if the same thing happens to you! 