I have an Intel SSD assigned as an A-Drive (the floppy format has been dead for at least 10 years) and that's where I store my AE & P-Pro Project files. Recently, something has been deleting the AE Project files (permanently deleting, as opposed to being able to recover them from the Trash). Still no problem with this in Premiere Pro CC, but this has happened twice to me in AE CC while using After Effects. As a hopeful fix, I've assigned the letter D to the drive and I have a suspicion this will correct this abhorrent behavior. I've submitted a bug report. Any one experience this?
There's a reason why the Windows configuration guide still advises to not use drive letters A and B... That's most likely Windows itself and has nothing to do with AE. Keep watching it and use tools like Sysinternals's System Monitor to keep an eye on file activity. I'm sure somewehre along the way there's simply some out of range errors for file allocation and the files simply are marked wrongly for overwriting...
Mylenium, thanks for that. What you're saying makes sense, but doesn't explain why I never had this problem with AE CS6 or even CS5. Also, the Premiere Pro project files on the same drive are left unscathed. It started with CC, so that's why I'm suspicious that it may be an AE issue. Like I said, I've changed the drive letter, and I'm quite confident that that will solve the problem.