.aep Files M.I.A!

I would really appreciate any input or help right now!
Situation:
I have been creating a showreel in AE, and saved many variations of my original file for each shot (like a template). The issue is I went to AME to render, and whilst it still does a mediocre and glitchy job at rendering the composition of source files, the actual source .aeps for each shot (the templated shot variations I mentioned earlier) are now all missing, and I fear many other have gone Missing In Action as well.
I feel like I am looking for the MH370 using specialist audio equipment with a pair of iphone earphones.
I have attached a full, dual monitor screenshot, with the right monitor displaying missing .aep files with a "blue orb" type icon, I am assuming indicating the files have gone offline.
Just to clarify - yes, the entire .aep files have gone missing, along with the folder containing them. However, some other files from folders untouched for over a week have decided to arbitrarily jump ship too.
I am just trying to make ends meet, all CC is doing is causing me hiccups, this really is horrible. CS5 was amazing.
System Info:
Windows 8.1 64bit via SSD
Adobe After Effects Version CC 12.2.1.5 (64bit)
Adobe Media Encoder Version CC 7.2.0.43 (64bit)

I thought I would just bump this thread, considering there are items at the top of the list that have been solved

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