Seems you’ve already “lost it”.
Where is your work stored? Location?
What backup regime do you follow?
Answer is: No, your work is generally stored away from the app–like Word docs are stored away from the Word application, unless a user does something quirky, like unhiding AppsData\Local and messing around there.
Simply say where your work is stored so you can stop getting 150 shot in the dark responses–you may like that.
Okay, I don’t understand why the location of my saves is important if it is in the Backup preferences, but here goes. But you also asked about the backup regime. Typically, I just close the project at the end of the day, and all except for the once-a-week, it launches the next day.
Using the File Explorer:
C:\Users(Me)\AppData\Local\LiteratureAndLatte\Scrivener\Backups(Project)
Backups(Project).scriv
Oddly, however, after that, also under the Backup folder, there is a set of zipped folders, the most recent of which also contains an unzipped folder with my project file. So I seem to have two backups, the first of which, is not under a zipped folder.
But when I “Open Backup Folder” in the Project Backup preference window within my project, it shows ; “Quick access” and the most recent list of Zipped folders and one unzipped folder. The unzipped folder is not yesterday’s save, but the day before.
Your backup pathway looks unusual and should not have unzipped folders there if check the option to store backup as a zip file. Perhaps you should choose another location to store your backups and away from the folder storing your active projects. Here is what my current setup using the Google drive to store zip backups look like and my backup settings as well.
I store my Scrivener files as below. You’ve mixed up working projects with backups and is the source of your losing the “manuscript” I’m guessing. Hence from start we were asking you these questions.
: Projects all in ~\documents\scrivener
: All backups as “zip” files, keeping 25 copies in ~\backups\scrivener
Backups must not be in same folder as working projects. Scrivener will not open backups, which must be unzipped to be opened.
I rely on system backups to backup both above. I recall you say above that you don’t use cloud services (although I would not rely on storing stuff in synced cloud services)
Okay. We may be getting somewhere. I think what this means is that I should make a new ‘Scrivener’ folder under “Documents” in the File Explorer, do manual saves, AND in the File>Options> Backup menu, check the box that says “Back up with each manual save”. Then I can delete the non-zipped backup folders. Is that right?
But why 25 backup copies? Is this to accommodate multiple projects?
Make sure the backup options match the way you work. A backup that only runs when Scrivener closes won’t help much if you leave Scrivener open for days at a time. A manual save every page or two will quickly fill up the maximum number of backups. (Which is per project, not total.)
If you have some other form of system backup – and you should! – that will also have copies of your Scrivener backups, so you may not need to keep as many.
Wh
Why do you think you have to do manual saves? Where is that idea coming from?
Scrivener will automatically save the current file you are working with on close and (default) every time it detects 2 seconds of inactivity, eg thinking or sipping coffee.
yes you can get rid of non zipped backups but maybe some of this are active projects? careful. be careful.
I have backups set to get created on each project open and close . i never do manual saves and thus no backups on non existent manual saves. I save 25 backups since the cost to do so is trivial. I worry about other things.
No. Each project has it’s own backup count. Older backups for that particular project will be be purged when that count is exceeded.
Here’s why: What typically happens when you have an issue with a Scrivener project, for example if your project gets corrupted for some reason, is that you will open and close the project multiple times trying to figure out what’s wrong. Each time you do that Scrivener will make a backup of your corrupted project, and at the same time it will delete your oldest good backup, thus effectively replacing a good backup with a corrupted one. With the default of 5, by opening and closing your project 5 times, you can quickly end up with only corrupted backups. I cannot tell you how many times I’ve seen posters do this to themselves and permanently lose words. Changing the setting to 25 is a cheap way to buy yourself some margin, because when you are slammed by a data issue, you don’t want to have to also contend with the loss of your most recent good backups.
I have mine set to “keep all”, because I don’t want the software making those kind of decisions for me. At the start of every month I purge backups myself.
I got the impression upthread that the OP’s habit is to leave the project open all day long. In this scenario, incorporating manual saves is a great idea.
Oh. Long thread. That being said leaving project open all day not something that would occur to me to do and if so I wouldn’t do. 
Edit. I cap at 25 backups. But I get and agree with your points. I rely on my system backups that go back weeks and months if I really need to recover something. Never had corruption issues. But problems caused between chair and keyboard happen.
I have always liked manual backups because stuff happens, often without warning, like power outages, which is why I’d really like to have a ‘Save’ icon available in a toolbar. But that 2-second auto save is an excellent substitute.
But all this still doesn’t answer my original question, which I now modify as; Why does Scrivener refuse to find my projects on Thursday mornings? All other days all I have to do is launch from the Windows Start Menu. But not on Thursdays. At least it was Thursday this week. I’d like to know what is screwed up in my setup.
Maybe I should delete all backups, except today’s (and maybe yesterday’s) and hope whatever it is goes away.
If the question to which you refer is “how do I discover that it is missing”, then the answer is, I launch Scrivener as always from the Start Menu, and a popup tells me that it can’t locate the project. So, no procedure, just a normal launch which usually works, but sometimes doesn’t. At that point I have to cancel the launch, go root around in the File Explorer and unzip the previous night’s backup.
As explained above, something is moving the project. If Scrivener says it can’t find it, then it is not in the location from which Scrivener last successfully opened it.
Having an unzipped project in your backup folder is potentially a clue, suggesting that some operation – either manual or automated – is putting the active project in a location where it would not normally be.
To troubleshoot in more detail, though, we would need to know where you think the project is stored, what other software is running on your system, what happens if you search for the project (not the backup) after this happens, and so on.
My project opened correctly this morning, but following the trail listed at the top of the window (above the menu bar) is another mystery. It shows that the project is under the Documents>Scrivener manuscripts - Scrivener menu in Windows, and, opening the File Explorer to track it, it shows the correct date and time. The Type is “Scrivener Project” but the Size (not compressed size) is only 153 KB, which is about 32,000 KB too small at this point, as listed under the >AppData>Local>LiteratureAndLatte>Scrivener>Backup folder.
Other oddities: I started to work on this project a long time ago, but didn’t start to get serious until I purchased Scrivener 3. My initial scribbles began using Word and also WordPerfect, but I haven’t even launched WordPerfect in months, perhaps even a year, yet in the same folder as the “Scrivener manuscript” (listed that way though it is not the name of my project) both of my old Word and WordPerfect files are listed as having been modified as of yesterday.
I would very much like to delete all the extraneous copies of my project, so if someone would tell me how the Scrivener algorithm saves by default, maybe I can resolve this stuff directly.
I will see if anything changes after my next Save, but Yesterday another oddity happened. I was trying to make a new character, but the New Character template opened with a blank template. After several attempts, I finally got the template to show the template, but the fact that it tried to fight me is worrying.
As for other software, typically I might have my browser open (DuckDuckGo) and perhaps Word and Kindle, which I use for background details (research done before Scrivener).
Being the genius strategist that I am, I have now started a new test project, just to see what Scrivener does with it. I also did what is usually an automatic weekly backup today, and now know where Scrivener likes to hide things. With luck I may be nearing my tribulations. Time will tell.
Still wonder about that weird New Character template glitch, though.
What software is this? The name of the product please.
Do you run any software that does PC cleanup? Name of product please.
Also, in your use of Scrivener, do you ever use the File > Save As command? If so, under what circumstances and what are your project naming conventions?
The OP never answer basic questions.
It’s useless trying to make sense of his setup.
Please clarify what you mean by “same folder.” Are they in the /Documents/Scrivener manuscripts folder? Or are they in the /Documents/Scrivener manuscripts/[project name].scriv folder?
Scrivener creates a folder ([projectname].scriv) in the location you specify, and puts the entire contents of the project in that folder. That location is “permanent,” in that Scrivener itself does not and cannot change it without direct instructions from the user.
It seems to me, though, that you don’t currently know which copies of the project are extraneous, so deleting anything before you resolve your current issue would be a terrible idea.
It all depends where you’ve saved them.
Given you’re an admitted Newbie I’m happy to offer a free 15 minute Zoom or Webex session to guide you through getting rid of the projects you want to delete and ensuring the save and backup strategies are solid. I do paid remote assistance, so I’m familiar with remote assistance, especially on Apple (trained Apple advisors on how to do remote sessions with Apple internal tools). 15 minutes should be more than sufficient.
