After Effects & Replacing Project Files into Personal Files

I'm not sure what is causing the problem but I have a workflow suggestion for you. AEP files are usually very small. I almost never overwrite files, I save versions. I have specific naming conventions that I have used since I started in the motion picture industry. It was taught to me by a master editor and it is the naming system used for many years by most if not all of the major studios. It has saved me thousands of hours over my career because I can always go back to a previous version if my client or a director wants to see something again. Everything is arranged and named by project, scene, and shot and take. 

I'm also confused by your statement "I started to copy and paste my After Effects projects onto my desktop and then start editing from my desktop instead of opening projects directly from my hard drive (it's safer this way to avoid any corruption on my hard drive)."  Your desktop is on a hard drive and it is just as easy to corrupt as any other drive. I understand using a working directory and an archive directory on another drive, but unless you also move footage around, any file you copy and paste to another location will lose all links to all footage in the project. The only way to avoid that is to do a Save As from inside AE. Just copying and moving AEP files will always foul up projects that have any linked assets in the project.

As far as your OS is concerned, it's just some file with data in it. You may be barking up the wrong tree when asking the AE devs to "fix" whatever you see. The only thing they have control over is anything happening from within AE and indeed there appear to be some data corruption issues lately under some conditions. The rest we can't know. Despite your long write up you have pretty much not provided a single bit of useful info like basic system info, types of drives used, contents of the projects and so on. Without that nobody can even make the crudest guess...

Mylenium

Also, this is not the first time something fishy happened. From time to time, I'll return to an older project, and I know that I made some small fixes and theyre missing when I reurn to a project. I am constantly saving my projects ontop of having the autsave turned on. So I'm just really unsure why some things don't get replaced or saved. And I think this replacing of the files is part of the problem.