It’s impossible to say what has happened, but let’s be sure of the current situation:
If the raw photos are gone except for a backup of them elsewhere then you’ve actually manually deleted them in LR with a command of some sort and chosen to remove the file from disk and not just remove the settings from the LR database.
If the LR folders aren’t in LR but the folders are still on the disk and the photos are in the folders on disk, then it seems like a catalog issue.
LR does continue doing things in the background for a few seconds after the UI goes away so it’s possible if the machine was shut off at the wrong time or put to sleep by shutting the lid then not reawakened but cold-booted, instead. SSDs do fail so perhaps a bad error happened in a crucial area of the catalog.
Assuming it’s just a catalog issue, do you mean you’ve never answered Yes to LR’s question to do a backup at Exit? If you have then you could merely open one of those backups and only redo what’s newer than the last backup. You would want to copy the backup .lrcat file to another folder so as not to overwrite the actual backup in case there is something wrong. Also make sure you’re not accidentally opening a backup file that’s 6 months old.
If you have no backups, do you have Auto Write XMP Metadata turned on in Preferences? If so then whenever you try to Import the lost photos, the initial settings would be whatever they were the last time XMP data was written.
I was looking for an explanation because I have 'lost' my photos as well and came across this Post. However, after reading ssprengel comment about a catalog I went to the 'file' in lightroom, opened 'open recent' and found 3 catalogues (which I had no idea that I had). When I opened (which involves relaunching) and checked the 3 catlogues, I found my missing 10,000 photos in one of the catogues. Huge relief. I am posting this if someone else, who isn't lightroom savy has a similar challenge.