Force App Store to re-download OS X.

When Apple releases a massive update, I always re-download the latest OS X installer from App Store, which I use to create an up-to-date USB recovery installer.

For you to re-download El Capitan (and, in general, any OS X version you have already installed), you need to open up App Store and go to Purchased.

Afterward, you click Download and, after answering Yes to a confirmation pop-up, the download will start.

That's how I've always done so far.

However, you might at times experience some issues while doing that.

This time around, in fact, El Capitan installer was grayed out and displayed as Downloaded. 

On a forum thread I found out the problem was caused by the older installer, which still was in the Applications folder.

After removing it, quitting and re-opening App Store, I was able to successfully start the download.

Hope it helps you solve similar issues.