I have used a certain 10 minute HD clip, then used that clip for a different project. AE has overwritten my old videos using this clip, and the roto-brush work from the original video is now gone.
Let me make sure that I understand what you're saying:
You rendered and exported a movie to a file. Then you rendered and exported a movie to a file again. And the second one replaced the first one?
Did you render and export the second movie to the same name and same location as the first? If so, then don't do that; instead specify a different file name and location for your new output files.
See this page for instructions on setting the name and location for output files.
If you're new to After Effects, I strongly recommend that you begin here:
Sorry, I guess I was just a little brief in my description. Let me try to get into a little more detail. I have 2 projects I am working on for a video game website. The first is an advertisement introduction video, the second is a seperate advertisement video. In the first video, I used a 10 minute clip that I intend on using for both projects. I spent some time roto-scoping out part of the video, to use in the first Ad. It came out exactly how I wanted it, rendered the file out as Intro_Short.mov. I moved on to the second Ad video and used this same clip again, only a different time frame in the clip. I spent hours roto-scoping out a different aspect of the clip. Once I completed the 2nd Ad, I rendered it out as Ad_True_Color.mov. Apparently, as I made changes to the new video, my old videos using that same footage, have been overwritten to the new roto-brush use. I have made numerous drafts and copies of each, and Ae is somehow overwriting the previously rendered files. I am very confused, and wish it were as simple as saving two files by the same name. Thank You very much for your time. I appreciate it alot. I think this is gonna make me lose my mind.
If there were two separate projects there is no way that your original footage could have been effected. There is no way possible for After Effects to alter the original footage.
If the Intro_Short.mov composition and the Ad_True_Color.mov composition were both inside the same project and both composition shared a nested or pre-composed layer then changing the shared comp would change both of your renders.
If you rendered the Intro_Short.mov then changing anything in the original comp, the roto work, or any other composition could not change the rendered movie unless you chose to overwrite the first render. After Effects cannot generate a reference movie from the render cue.
There must have been a user error somewhere in your workflow.