To start, there’s a vocabulary issue we need to straighten out:
Scrivener automatically commits your text to disk when you pause for a couple of seconds. That’s what “save” means in the context of Scrivener. There is a menu “File->Save” which invokes this feature, but by the time you can invoke it, your most recent edit is probably already saved to your hard drive since you stopped typing, even if you’re just using “CMD-s” to “save”.
“Backups” in the context of Scrivener refer to the file produced either through the settings in Scrivener->Preferences->Backup, or via the File->Back up->Back Up To… menu. Check out the former, and you’ll see where the “automatic” backups are stored. There will also be a button open the Finder in that location. Make copies of those files ASAP, because by default, only 5 of the most recent are kept, and they’re replaced every time you close a project (by default).
As for the File->Back up->Back Up to… menu, that’s how you can create your own “manual” backups. I like to make “milestone” backups when I complete a first draft, do a major edit, etc… and otherwise let the automatic backups do their jobs. I also use a Time Machine backup drive so I can get to any old automatic backups for as far back they persist.
What I suspect you are talking about when it comes to your lost backups is that you use the menu “File->Save As” to create a backup. I don’t know how those copies could disappear (have you done a search using the finder, or are you just using the list of recent projects in the Scrivener menu?), but I can tell you that a common problem that arises from using that menu to create backups is that the person working on their project continues their work in the backup copy, so that when they return to the “main” project, it looks like their most recent work is missing.
Also note: the .scrivx file (however it is that you’re finding that file) is just a index of all of the content of your project; it’s like the card catalog of a library. If you save a card catalogue from a fire, but leave the books, you still won’t have anything to read. Likewise, if you recover just the .scrivx file from your project, the actual text of your documents within the project will still be missing.
So, with all that out of the way… can you re-state your issue in terms of how you created your backups, how you “saved” and where all of these files are supposed to be in your estimation?