Was your vault folder in app’s system folder ( %APPDATA%\Obsidian\ )?
Any update would delete your additions to that folder: How Obsidian stores data - Obsidian Help
Hi, kshivner. I assume you’re asking me since mine is the only comment between your two comments. If my assumption is incorrect, feel free to tell me and to clarify.
I was responding to Jacinto, to help them figure out what deleted their vault. I wasn’t suggesting anything to you.
Before you write this off completely, did you check the recycle bin? Windows sometimes moves deleted folders there even if you’re not sure how they got deleted. Long shot but worth five seconds to look before settling for the backup.
Obsidian installation/upgrade to do not delete vaults (there is no code for that)
where is vault located exactly?
%USERPROFILE%\Obsidian
was the first thing I tried. 
%USERPROFILE%\obsidian
Is it possible you have %USERPROFILE% configured to be backed up in OneDrive, or any other cloud tool?
Do you have any filesystem cleaner apps installed, that may have “cleaned” the folder for you?
If you have an anti-virus tool, maybe the logs show some activity cleaning up that folder?
I finally found my BIG MISTAKE that caused all these problems:
Sort version: I configured the obsidian application installation folder to %userprofile%/Obsidian. Update or uninstall obsidian uses “Uninstall Obsidian.exe” that deletes every file in installation folder.
Long version: I now know why my Obsidian vault got deleted upgrading to version 1.13. I’ve just managed to delete it again by accident, and this time I actually watched the files disappearing right in front of my eyes without being able to stop it. I think I may have lost another week of work 
, unless I can recover the Sync instance that I paid for and configured yesterday.
But at least I now know the root cause. For some reason that I can’t remember, I told the installer to put the application in %userprofile%\Obsidian, which also happens to be where I store my vault. MASSIVE MISTAKE. (I think I really need a vacation, ASAP.)
When I updated Obsidian to 1.13, it uses the uninstaller “Uninstall Obsidian.exe” for the current version, and that uninstaller deletes the entire contents of the folder where the application was installed. Yesterday, Sync failed while trying to synchronize obsidian.exe because the file is larger than 200 MB, and was on my vault folder!!!. I noticed that in the logs today. So I decided to uninstall Obsidian and reinstall it in the correct location. I assumed that uninstall only delete the application files from a list of installed files, and I was wrong. The uninstaller then had the audacity to show me, file by file, everything it was deleting… which turned out to be my entire vault. 
Lessons learned: backup and sync your valuable data before do anything.
Anyway, I’m embarrassed to post this publicly, but I think I should. I debt to you.
Thank you all for your help trying to solve this nightmare.