Marco,
With hard drives as cheap as they are now, you can afford to have several just for archiving, You could use one for primary and one for backup. As they’d just sit on shelf ’til you need to re-activate the project, it is highly unlikely they’d go down, but then you’d have the backup too.
Another suggestion which I do a lot, is just re-render the files from AE when you need them. If it’s a long render, do it an night or over the weekend.
Finally, you can cut the files in QT Pro, they don’t have to be the same length, just pick a cut or other notable occurance somewhere near the middle, and copy and paste each half into a new QT file with a few frames of handle on either side. It’s pretty painless to do a match frame on the two pieces to reuse them. I do this method all the time, but, I am also using the drive storage method more and more.