Pavlos gave you the "proper" answer, regarding setting up such that, when you click on "Add", it would remember the last place you selected your wallpaper from.
Whichever one you choose, will become your wallpaper.
Why you wallpaper(s) disappeared from the settings could be a result of your having reinstalled (not upgraded) your OS, and MATE reset itself to defaults.
Otherwise, if you either renamed your directory from something else to My_Wallpapers, or you renamed the wallpaper file itself, the Preferences would determine the "wallpaper resource" (i.e. your previously selected wallpaper) has an invalid PATH definition (MATE working with pointers/references, not with actual files), so it automatically removes the offending reference, hence it going "poof" from the choices presented.
Also if you move the wallpaper to a different folder it will disappear. Say you just have it in the Pictures folder, then decide to organize and make a Wallpaper folder and move it that folder, it will disappear until you manually locate it again. I learned that through experience. Again the path is then wrong.