Im trying my best not to swear at this ************* program! Ive spent months building a spaceship scene, I was working on it yesterday and no issues, it was fine! Today, not so much. about 90 percent of the entire scene which includes hundreds, if not thousands, of objects with meshes on them have missing mesh. The hierarchy is still intact but all the meshes are MISSING!!! I didn’t change their location or anything like that, it just happened overnight and that really really sucks. I can manually select the game objects in the inspector and where it says missing mesh I can manually find them all again but its going to take days if not weeks. Has anyone else ever experienced this? WHY??? 
Close Unity and try going to the Project Folder, rename the Library Folder to something like LibraryOLD.
Open Unity up, (it may take awhile) but it will rebuild all the connections to prefabs, objects, etc.
That MIGHT help, MAYBE.
It has fixed all errors I’ve had so far.
I’m almost always scared to shut down Unity after a save, so I just leave it on, because Unity won’t always save my level and wam, it doesn’t even exist whatsoevver anymore.
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Ok ill try anything at this point, thanks for giving me a glimmer of hope in this horrible situation.
Unfortunately it didn’t work. It loaded for a while and my hopes peaked in anticipation 
but as fate would have it, no luck. I just wonder how it happened and what if it happens again? Ill keep wasting days and days manually finding each little piece of mesh. I hope this was a one off freak accident/bug. Wouldn’t wish this on anyone:(
Ive noticed that there are 2 instances of each mesh in the assets folder. Very odd.
No backups?
It is amazing the number of people who don’t back up their projects on a regular basis. At the very least you should be doing this daily. Ideally you would have a version control system in addition to regular backups. Don’t keep them all in the same location either.
Don’t assume this will be a one time thing. Data loss is pretty common and can be caused by many different things.
Yeah I backed it up 7 days ago so it wasn’t all lost but I’ve certainly learned to do more backups. Never imagined something like this could happen though. But It looked worse then it is, It’ll take the rest of the day to fix but at least there is a fix and I won’t loose anything Ive made thank goodness.
I’ve thought the same thing whenever I had to forcibly restart Windows and some program lost its configuration files. It almost never was the program causing the crash either.
I got off with the scare this time there wasn’t a crash at any point though thats whats baffling. It literally happened overnight.